<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" "journalpublishing.dtd">
<article xml:lang="EN" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article">
<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title>Frontiers in Plant Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Plant Sci.</abbrev-journal-title>
<issn pub-type="epub">1664-462X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2022.830931</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Plant Science</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Modifying Anthocyanins Biosynthesis in Tomato Hairy Roots: A Test Bed for Plant Resistance to Ionizing Radiation and Antioxidant Properties in Space</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<name><surname>Massa</surname> <given-names>Silvia</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="corresp" rid="c001"><sup>&#x002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/261102/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Pagliarello</surname> <given-names>Riccardo</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1555593/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Cemmi</surname> <given-names>Alessia</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1626512/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Di Sarcina</surname> <given-names>Ilaria</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Bombarely</surname> <given-names>Aureliano</given-names></name>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Demurtas</surname> <given-names>Olivia Costantina</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/260586/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Diretto</surname> <given-names>Gianfranco</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/267882/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Paolini</surname> <given-names>Francesca</given-names></name>
<xref ref-type="aff" rid="aff5"><sup>5</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/543735/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Petzold</surname> <given-names>H. Earl</given-names></name>
<xref ref-type="aff" rid="aff6"><sup>6</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Bliek</surname> <given-names>Mattijs</given-names></name>
<xref ref-type="aff" rid="aff7"><sup>7</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Bennici</surname> <given-names>Elisabetta</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1649383/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Del Fiore</surname> <given-names>Antonella</given-names></name>
<xref ref-type="aff" rid="aff8"><sup>8</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1614543/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>De Rossi</surname> <given-names>Patrizia</given-names></name>
<xref ref-type="aff" rid="aff9"><sup>9</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/996229/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Spelt</surname> <given-names>Cornelis</given-names></name>
<xref ref-type="aff" rid="aff7"><sup>7</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Koes</surname> <given-names>Ronald</given-names></name>
<xref ref-type="aff" rid="aff7"><sup>7</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Quattrocchio</surname> <given-names>Francesca</given-names></name>
<xref ref-type="aff" rid="aff7"><sup>7</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/285429/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Benvenuto</surname> <given-names>Eugenio</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/212345/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department for Sustainability, Biotechnology and Agro-Industry Division &#x2013; Biotec Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development</institution>, <addr-line>Rome</addr-line>, <country>Italy</country></aff>
<aff id="aff2"><sup>2</sup><institution>Department of Agriculture and Forest Sciences, University of Tuscia</institution>, <addr-line>Viterbo</addr-line>, <country>Italy</country></aff>
<aff id="aff3"><sup>3</sup><institution>Fusion and Nuclear Safety Technologies Department, Italian National Agency for New Technologies, Energy and Sustainable Economic Development</institution>, <addr-line>Rome</addr-line>, <country>Italy</country></aff>
<aff id="aff4"><sup>4</sup><institution>Department of Biosciences, University of Milan</institution>, <addr-line>Milan</addr-line>, <country>Italy</country></aff>
<aff id="aff5"><sup>5</sup><institution>&#x2018;Regina Elena&#x2019; National Cancer Institute, HPV-UNIT, Department of Research, Advanced Diagnostic and Technological Innovation, Translational Research Functional Departmental Area</institution>, <addr-line>Rome</addr-line>, <country>Italy</country></aff>
<aff id="aff6"><sup>6</sup><institution>School of Plants and Environmental Sciences, Virginia Tech</institution>, <addr-line>Blacksburg, VA</addr-line>, <country>United States</country></aff>
<aff id="aff7"><sup>7</sup><institution>Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam</institution>, <addr-line>Amsterdam</addr-line>, <country>Netherlands</country></aff>
<aff id="aff8"><sup>8</sup><institution>Department for Sustainability, Biotechnology and Agro-Industry Division &#x2013; Agrifood Sustainability, Quality, and Safety Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development</institution>, <addr-line>Rome</addr-line>, <country>Italy</country></aff>
<aff id="aff9"><sup>9</sup><institution>Energy Efficiency Unit Department &#x2013; Northern Area Regions Laboratory, Casaccia Research Center, Italian National Agency for New Technologies, Energy and Sustainable Economic Development</institution>, <addr-line>Rome</addr-line>, <country>Italy</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Henrik Toft Simonsen, Technical University of Denmark, Denmark</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Concetta Licciardello, CREA Research Centre for Olive, Fruit and Citrus Crops, Italy; Zhengkun Qiu, South China Agricultural University, China</p></fn>
<corresp id="c001">&#x002A;Correspondence: Silvia Massa, <email>silvia.massa@enea.it</email></corresp>
<fn fn-type="other" id="fn004"><p>This article was submitted to Plant Biotechnology, a section of the journal Frontiers in Plant Science</p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>24</day>
<month>02</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>13</volume>
<elocation-id>830931</elocation-id>
<history>
<date date-type="received">
<day>07</day>
<month>12</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>07</day>
<month>01</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2022 Massa, Pagliarello, Cemmi, Di Sarcina, Bombarely, Demurtas, Diretto, Paolini, Petzold, Bliek, Bennici, Del Fiore, De Rossi, Spelt, Koes, Quattrocchio and Benvenuto.</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Massa, Pagliarello, Cemmi, Di Sarcina, Bombarely, Demurtas, Diretto, Paolini, Petzold, Bliek, Bennici, Del Fiore, De Rossi, Spelt, Koes, Quattrocchio and Benvenuto</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<abstract>
<p>Gene expression manipulation of specific metabolic pathways can be used to obtain bioaccumulation of valuable molecules and desired quality traits in plants. A single-gene approach to impact different traits would be greatly desirable in agrospace applications, where several aspects of plant physiology can be affected, influencing growth. In this work, MicroTom hairy root cultures expressing a MYB-like transcription factor that regulates the biosynthesis of anthocyanins in <italic>Petunia hybrida</italic> (<italic>PhAN4</italic>), were considered as a testbed for bio-fortified tomato whole plants aimed at agrospace applications. Ectopic expression of <italic>PhAN4</italic> promoted biosynthesis of anthocyanins, allowing to profile 5 major derivatives of delphinidin and petunidin together with pelargonidin and malvidin-based anthocyanins, unusual in tomato. Consistent with <italic>PhAN4</italic> features, transcriptomic profiling indicated upregulation of genes correlated to anthocyanin biosynthesis. Interestingly, a transcriptome reprogramming oriented to positive regulation of cell response to biotic, abiotic, and redox stimuli was evidenced. <italic>PhAN4</italic> hairy root cultures showed the significant capability to counteract reactive oxygen species (ROS) accumulation and protein misfolding upon high-dose gamma irradiation, which is among the most potent pro-oxidant stress that can be encountered in space. These results may have significance in the engineering of whole tomato plants that can benefit space agriculture.</p>
</abstract>
<kwd-group>
<kwd>MicroTom</kwd>
<kwd>hairy root cultures</kwd>
<kwd>agrospace</kwd>
<kwd>biofortification</kwd>
<kwd>anthocyanins</kwd>
<kwd>gamma radiation</kwd>
</kwd-group>
<contract-sponsor id="cn001">Agenzia Spaziale Italiana<named-content content-type="fundref-id">10.13039/501100003981</named-content></contract-sponsor>
<counts>
<fig-count count="10"/>
<table-count count="2"/>
<equation-count count="0"/>
<ref-count count="219"/>
<page-count count="30"/>
<word-count count="21405"/>
</counts>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="S1">
<title>Introduction</title>
<p>Anthocyanins are valuable water-soluble plant pigments. They accumulate in the vacuole of specialized cells and play a crucial role in pigmentation of flowers and fruits, pollinators attraction, plant-pathogen interaction, protection against ultraviolet (UV) light, and modulation of reactive oxygen species (ROS)-signaling both in reproductive and in vegetative tissues (<xref ref-type="bibr" rid="B24">Brunetti et al., 2013</xref>). As plant-derived molecules, anthocyanins are naturally present in the human diet where they are predominantly represented as glycosides, in a multitude of fruits and vegetables, among which berries and grapes have the highest content (<xref ref-type="bibr" rid="B19">Bognar et al., 2013</xref>). Anthocyanins act as health-promoting and chronic-diseases-preventing molecules, due to antioxidant, anti-inflammatory, anti-proliferative and anti-neurodegenerative functions (<xref ref-type="bibr" rid="B18">Blesso, 2019</xref>; <xref ref-type="bibr" rid="B99">Krga and Milenkovic, 2019</xref>; <xref ref-type="bibr" rid="B186">Tian et al., 2019</xref>; <xref ref-type="bibr" rid="B13">Bendokas et al., 2020</xref>; <xref ref-type="bibr" rid="B89">Kalt et al., 2020</xref>). Due to these properties, anthocyanins have increasing applications in the food sector and there is also growing interested in the design of food crops with improved levels and composition of these antioxidant nutraceuticals. In particular, the research involved in the definition of plants intended for &#x2018;agrospace&#x2019; applications, will have to tackle the issue to provide fresh and healthy food for space crews in the context of a harmful ionizing irradiated environment, and to cope with cultivation areas subjected to possible biotic contaminations, as well (<xref ref-type="bibr" rid="B5">Amalfitano et al., 2020</xref>; <xref ref-type="bibr" rid="B16">Bijlani et al., 2021</xref>). Agrospace crops are, therefore, candidates for the application of technologies aiming to improve both their content in antioxidant nutraceuticals and resistance to biotic and abiotic stresses (<xref ref-type="bibr" rid="B211">Zabel et al., 2015</xref>, <xref ref-type="bibr" rid="B210">2016</xref>; <xref ref-type="bibr" rid="B124">Massa et al., 2016</xref>; <xref ref-type="bibr" rid="B92">Khodadad et al., 2020</xref>).</p>
<p>Tomato (<italic>Solanum lycopersicum</italic> L.) is a rich source of bioactive molecules such as carotenoids (in particular, lycopene), polyphenols and flavonoids, ascorbic acid, and other vitamins (<xref ref-type="bibr" rid="B66">Gerszberg et al., 2015</xref>; <xref ref-type="bibr" rid="B123">Mart&#x00ED; et al., 2016</xref>). However, anthocyanins are poorly accumulated in cultivated tomatoes and even the fruits of cultivar harboring natural mutants for the <italic>Abg</italic> (<italic>Aubergine</italic>), <italic>Aft</italic> (<italic>Anthocyanin fruit</italic>), and <italic>Atv</italic> (<italic>Atroviolaceum</italic>) loci, only contain these molecules in the peel (<xref ref-type="bibr" rid="B130">Mes et al., 2008</xref>; <xref ref-type="bibr" rid="B70">Gonzali et al., 2009</xref>; <xref ref-type="bibr" rid="B149">Povero et al., 2011</xref>). Accumulation in fruit flesh and other organs upon genetic engineering indicates that tomatoes can be manipulated to this end (<xref ref-type="bibr" rid="B215">Zhang et al., 2014</xref>; <xref ref-type="bibr" rid="B116">Lloyd et al., 2017</xref>). By breeding, tomato lines were generated that combine the dominant <italic>Atv</italic> allele with <italic>Aft</italic> or <italic>Abg</italic>. These lines accumulated up to 0.1% (in fresh weight) of the anthocyanin petunidin-3-(p-coumaryl)-rutinoside-5-glucoside in the fruit epidermis (<xref ref-type="bibr" rid="B130">Mes et al., 2008</xref>; <xref ref-type="bibr" rid="B149">Povero et al., 2011</xref>). Gene and pathway engineering are powerful approaches to enhance the biosynthesis of anthocyanins in plants, and they have been successfully applied in food staples (<xref ref-type="bibr" rid="B65">Garg et al., 2018</xref>). Transcription factors, regulating the expression of structural biosynthetic genes, control the activity of the anthocyanin pathway in all plant species (<xref ref-type="bibr" rid="B69">Gonzalez et al., 2008</xref>). In particular, proteins belonging to specific clades of R2R3-MYB, bHLH, WDR, and WRKY have been shown to regulate anthocyanins biosynthesis combined in the MBWW transcription complex, as shown for a multitude of plant species among which tomato (<xref ref-type="bibr" rid="B153">Ramsay and Glover, 2005</xref>; <xref ref-type="bibr" rid="B215">Zhang et al., 2014</xref>; <xref ref-type="bibr" rid="B64">Gao et al., 2018</xref>). The combined expression of a MYB and bHLH regulators of the anthocyanin pathway from <italic>Antirrhinum majus</italic> (<italic>Delila</italic> and <italic>Rosea1</italic>, respectively) under a fruit-specific promoter, resulted in the production of anthocyanins in fruits peel and flesh of tomato (<xref ref-type="bibr" rid="B26">Butelli et al., 2008</xref>). Studies have demonstrated that pathway engineering approaches implying the sole use of MYB factors belonging to the SG6 clade are sufficient to restore the biosynthesis of anthocyanins by promotion of the transcription of their bHLH partners and, therefore, by reconstituting the MBWW (<xref ref-type="bibr" rid="B128">Mehrtens et al., 2005</xref>; <xref ref-type="bibr" rid="B182">Takos et al., 2006</xref>; <xref ref-type="bibr" rid="B212">Zhang et al., 2019</xref>). The tomato <italic>ANT1</italic> gene encodes a MYB transcription factor belonging to the SG6 clade, highly homologous to the <italic>Antirrhinum Rosea</italic>. It has been demonstrated that ectopic expression of <italic>ANT1</italic> from a tomato wild relative (<italic>S. chilense</italic>), induces purple spotting on the epidermis of tomatoes (<xref ref-type="bibr" rid="B125">Mathews et al., 2003</xref>; <xref ref-type="bibr" rid="B165">Schreiber et al., 2012</xref>). The 35S promoter-driven expression of either the <italic>Solanum lycopersicum ANT1</italic> or <italic>AN2</italic> (another SG6 MYB), has been shown to induce anthocyanins production in the flesh and peel of the fruit and different organs of tomato plants (<xref ref-type="bibr" rid="B93">Kiferle et al., 2015</xref>). Upon overexpression of <italic>SlAN2</italic>, together with anthocyanins accumulation in fruits, flower organs, and vegetative parts, an enhancement of the emission of volatile molecules contributing to the aroma of fruits was found, as well (<xref ref-type="bibr" rid="B88">Jian et al., 2019</xref>). In addition, <italic>SlAN2</italic> has been related to the variation of levels of specialized metabolites other than anthocyanins, and of fruit softening (<xref ref-type="bibr" rid="B122">Meng et al., 2015</xref>). These findings seem to confirm that MYB transcription factors of the SG6 clade can regulate various, sometimes unrelated, processes in tomatoes, as well (<xref ref-type="bibr" rid="B176">Stracke et al., 2001</xref>; <xref ref-type="bibr" rid="B218">Zimmermann et al., 2004</xref>; <xref ref-type="bibr" rid="B212">Zhang et al., 2019</xref>). Therefore, a SG6 MYB-based approach may be considered suitable to affect multiple pathways in tomatoes.</p>
<p>The <italic>Anthocyanin4</italic> gene of <italic>Petunia hybrida</italic> (<italic>PhAN4</italic>) is a SG6 member of a small family of genes encoding very similar MYBs phylogenetically related to the snapdragon <italic>AmROSEA</italic>, the tomato <italic>SlANT1</italic>, and other anthocyanin-regulating MYBs from a multitude of plant species. All these petunia MYBs are involved in the induction of anthocyanins accumulation in different plant parts and response to different stimuli (<xref ref-type="bibr" rid="B148">Povero, 2011</xref>). In the present study, we performed <italic>Agrobacterium rhizogenes</italic>-mediated transfer of a construct for the expression of <italic>PhAN4</italic> into the miniature tomato genotype MicroTom to generate hairy root cultures (HRCs). HRCs were intended as a testbed for whole plant engineering strategies able to improve traits for space cultivation. We previously reported about improved <italic>in vivo</italic> response to space-mimicking conditions (i.e., static magnetic fields and X and gamma rays) of <italic>PhAN4</italic>-engineered HRC (<xref ref-type="bibr" rid="B199">Villani et al., 2017</xref>; <xref ref-type="bibr" rid="B44">Desiderio et al., 2019</xref>), confirming that this plant-based expression system, used over the last 30 years to produce various specialized metabolites and recombinant proteins of pharmaceutical value (<xref ref-type="bibr" rid="B73">Gutierrez-Valdes et al., 2020</xref>; <xref ref-type="bibr" rid="B74">H&#x00E4;kkinen et al., 2020</xref>), is useful in studies on the adaptation of plants to extraterrestrial conditions, as well. Recently, HRCs served in several plant species as handier and faster biotechnology tools, compared to whole plant transformation, to gain biological insights in gene function, spatial and temporal gene expression studies, and signaling pathways in plant cell response to a changing environment (<xref ref-type="bibr" rid="B157">Ron et al., 2014</xref>).</p>
<p>Anthocyanin biosynthesis engineering in HRCs was reported in a few species (<xref ref-type="bibr" rid="B171">Sharma et al., 2013</xref>; <xref ref-type="bibr" rid="B108">Li et al., 2016</xref>; <xref ref-type="bibr" rid="B185">Thwe et al., 2016</xref>; <xref ref-type="bibr" rid="B80">Hou et al., 2017</xref>), and, to date, never in tomatoes. In this study, <italic>PhAN4</italic> gene expression resulted in anthocyanins accumulation in tomato HRCs. Transcript profiling showed that several genes encoding enzymes and transcription factors involved in anthocyanins biosynthesis were upregulated. Interestingly, also genes correlated to cell response to biotic and abiotic stress, including redox stimuli, resulted in transcriptionally upregulated.</p>
<p>In addition, we report about the antioxidant properties and diminished generation of ROS in HRCs expressing <italic>PhAN4</italic> exposed to ionizing gamma radiation. <italic>PhAN4</italic> HRCs were endowed with a ninefold enhanced antioxidant capacity <italic>per se</italic> compared to controls by 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. Furthermore, ROS accumulation was counteracted after gamma radiation, as shown by Electron Spin Resonance (ESR) Spectroscopy. Both UV-VIS spectra and photoluminescence analysis demonstrated that polyphenols content and stability of soluble protein folding were not significantly affected by high dose gamma irradiation in <italic>PhAN4</italic>-engineered HRCs compared to control.</p>
<p>In conclusion, MicroTom HRCs represented a simplified model that allowed to rapidly test <italic>PhAN4</italic> expression effects on tomato cells, possibly opening the way to the application of the strategy to the engineering of whole plants intended for cultivation in harsh environments like future space outposts.</p>
</sec>
<sec id="S2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="S2.SS1">
<title>Gene and Constructs</title>
<p><italic>Anthocyanin4</italic> (<italic>PhAN4</italic>) complementary DNA (cDNA) from petals of <italic>Petunia</italic> &#x00D7; hybrida cultivar Violet 30 (GenBank: HQ428105.1) was amplified with primers containing AttB sites and recombined into pDONR221 (RU Ghent) to produce an entry clone. This was then recombined with pKGW,0 (RU Ghent) to produce the 35S:AN4 construct and in pK7FWG2 (RU Ghent) to yield the 35S:GFP-<italic>PhAN4</italic> construct (where the <italic>GFP</italic> gene fusion was adopted to possibly stabilize the PhAN4 transcription factor).</p>
</sec>
<sec id="S2.SS2">
<title>Hairy Root Cultures Generation</title>
<p><italic>Solanum lycopersicum</italic> (cv. MicroTom) clonal hairy root lines were obtained from wild-type leaf explants by infection with <italic>A. rhizogenes</italic> A4 (ATCC, 43057&#x2122;) harboring either the 35S:<italic>PhAN4</italic> or the 35S:GFP-<italic>PhAN4</italic> or no additional construct. Bacteria were grown in a YEB medium with 50 &#x03BC;g/ml rifampicin and 50 &#x03BC;g/ml kanamycin at 28&#x00B0;C and 220 rpm to OD600 = 0.6. Bacteria were centrifuged at 3,000 &#x00D7; <italic>g</italic> for 15 min and resuspended at OD<sub>600</sub> = 1 in Murashige and Skoog medium (MS, Duchefa) with 30 g/l sucrose and 200 &#x03BC;M acetosyringone, pH 5.8. Leaves from 3-week-old MicroTom plants were harvested, sterilized in 0.1% (v/v) sodium hypochlorite solution for 15 min, and aseptically cut into explants of 1 cm &#x00D7; 1 cm. Explants were immersed in the recombinant <italic>A. rhizogenes</italic> suspension for 15 min, in a rotary shaker at the minimum speed, and in the dark. Explants were dried onto sterilized tissue paper and transferred on their adaxial side, on MS agar medium co-culture plates with 100 &#x03BC;M acetosyringone and incubated in the dark for 4 days. Explants were then blotted and transferred to MS medium supplemented with 250 &#x03BC;g/ml cefotaxime (Cef) at 25&#x00B0;C. Fresh growing hairy roots were obtained after 8&#x2013;10 days. Emerging roots of 1 cm in length were excised and transferred to new plates. <italic>A. rhizogenes</italic> was eliminated with decreasing Cef concentrations (0.25, 0.125, and 0.05 &#x03BC;g/ml) until no antibiotic was added. HRCs were screened for pigmentation under a dissecting microscope. Growth was estimated by the increase in fresh weight at different time points after subculture over a 28-day culture period recorded for three biological replicates for chosen hairy root clones. Hairy root biomass harvested for analysis was carefully handled, pulverized in liquid nitrogen, and immediately stored at &#x2212;80&#x00B0;C. For metabolite content and antioxidant properties analysis, HRCs were lyophilized in a freeze-dry system (FreeZone Labconco, Kansas City, MO, United States).</p>
</sec>
<sec id="S2.SS3">
<title>Polymerase Chain Reaction Assays</title>
<p>Standard polymerase chain reaction (PCR) assays were performed on genomic DNA of kanamycin-resistant hairy root clones (extracted with NucleoSpin Plant II Kit; Macherey-Nagel; Duren, Germany) with primers specific for <italic>PhAN4</italic>, <italic>rol B, rol C</italic>, <italic>virC1</italic>, respectively (<xref ref-type="supplementary-material" rid="TS1">Supplementary Table 1</xref>), to select hairy root lines carrying <italic>PhAN4</italic> transgene clean from <italic>A. rhizogenes</italic> in the tissue culture. In selected HRC clones, SYBR Green real-time PCR was used to determine the <italic>PhAN4</italic> copy number. The tomato actin 41 gene (NCBI Reference Sequence: NM_001330119.1) served as an endogenous gene reference. For qPCR (i-Cycler iQ detection system; BioRad Laboratories Inc., Milan, Italy) Kapa SYBR Fast 2&#x00D7; qPCR Master Mix (KAPA Biosystems, Milano, Italy) was used, according to the manufacturer&#x2019;s instructions. Samples were amplified at 95&#x00B0;C for 3 min, followed by 40 cycles of denaturation at 95&#x00B0;C for 15 s, annealing, and extension at 60&#x00B0;C for 30 s.</p>
<p>Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen; Valencia, CA, United States) and then treated with amplification grade DNaseI (Invitrogen, Cambridge, MA, United States). cDNA was synthesized using the iScript&#x2122; cDNA Synthesis Kit (BioRad Laboratories Inc., Milan, Italy) and used as a template for real time-PCR analysis (Kapa SYBR Fast 2&#x00D7; qPCR Master Mix; KAPA Biosystems, Milan, Italy) in iCycler iQ detection system (BioRad Laboratories Inc., Milan, Italy). The actin 41 gene was used as the reference gene. Primers are listed in <xref ref-type="supplementary-material" rid="TS1">Supplementary Table 1</xref>. Relative gene expression levels were obtained using the 2<sup>&#x2013;&#x0394;CT</sup> formula (<xref ref-type="bibr" rid="B115">Livak and Schmittgen, 2001</xref>).</p>
</sec>
<sec id="S2.SS4">
<title>Phenylpropanoids Identification</title>
<p>Anthocyanin profile was carried out on representative <italic>PhAN4</italic> and GFP-<italic>PhAN4</italic> HRCs by liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) as reported before (<xref ref-type="bibr" rid="B46">Diretto et al., 2019</xref>; <xref ref-type="bibr" rid="B29">Carmona et al., 2021</xref>) with slight modifications. Briefly, 3 mg (dried weight) of ground hairy roots were re-suspended in 600 &#x03BC;l of 85:15 MeOH: 1N HCl, vortexed, shaken in Mixer Mill (MM) for 15&#x2032; at 20 Hz frequency and gently mixed at 4&#x00B0;C O.N. Samples were then centrifuged at 20,000 &#x00D7; <italic>g</italic> for 20 min, the supernatant recovered, completely dried and re-suspended in 600 &#x03BC;l of spiked (with 0.5 &#x03BC;g/ml formononetin, as internal standard) 75% MeOH + 0.1% formic acid. Samples were then centrifuged 10 min at 20,000 &#x00D7; <italic>g</italic> at RT, and the supernatant was transferred to HPLC vials for MS analysis with a Q-Exactive mass spectrometer (Thermo Fisher Scientific, Cambridge, MA, United States), coupled to a HPLC system equipped with a photodiode array detector (Dionex, Califiornia, United States). LC separation of anthocyanins was performed injecting 5 &#x03BC;l of sample on a C18 Luna reverse-phase column (100 &#x00D7; 2.1 mm, 2.5 &#x03BC;m; Phenomenex, Torrance, CA, United States), using as mobile phase water + 0.1% formic acid (A) and acetonitrile + 0.1% formic acid (B) at a total flow rate of 250 &#x03BC;l/min. The separation was developed using 5% B for 0.5 min, followed by a 24 min linear gradient to 75% B. The ionization was performed using heated electrospray ionization (HESI) source, with nitrogen used as sheath and auxiliary gas, and set to 35 and 10 units, respectively. The vaporizer temperature was 250&#x00B0;C, the capillary temperature was 30&#x00B0;C, the spray voltage was set to 3.5 kV, the probe heater temperature was 390&#x00B0;C, and the S-lens RF level was set at 50. The acquisition was performed in the mass range 110/1,600 m/z both in positive and in negative ion mode with the following parameters: resolution 70,000, microscan 1, AGC target 1e6, maximum injection time 50. UV-VIS detection was continuous from 220 to 700 nm. All solvents used were LC-MS grade (Merck Millipore, Burlington, MA, United States). Identification was achieved based on accurate masses and by comparison with authentic reference substances. The ion peak areas were normalized to the ion peak area of the internal standard (formononetin).</p>
<p>Total anthocyanins content was measured by spectrophotometric analysis, as described in the study of <xref ref-type="bibr" rid="B23">Brito et al. (2014)</xref>, using the extinction coefficient of the most abundant anthocyanin (petunidin-3-(p-coumaroyl)-rutinoside-5-glucoside).</p>
</sec>
<sec id="S2.SS5">
<title>Determination of the Total Phenolics Accumulation Level</title>
<p>Total phenolic content of representative <italic>PhAN4</italic> and GFP-<italic>PhAN4</italic> MicroTom HRC was estimated by colorimetric assay with modified (<xref ref-type="bibr" rid="B85">Inglett et al., 2010</xref>) Folin&#x2013;Ciocalteu reagent (Merk, Germany) (<xref ref-type="bibr" rid="B168">&#x015E;ensoy et al., 2006</xref>). Briefly, 4.25 ml of de-ionized water was mixed with 0.25 ml of ethanolic extract diluted 1:5 with 80% (v/v) ethanol and 0.25 ml of Folin-Ciocalteu reagent. After 7 min incubation in the dark at room temperature, 0.5 ml of saturated sodium carbonate solution (20%) was added, and the mixture was incubated for 40 min in the dark at room temperature. Absorbance was measured at 725 nm using a UV-VIS spectrophotometer (PerkinElmer, Waltham, MA, United States). A standard curve was prepared with gallic acid, as the reference standard. Final values were obtained by interpolating the absorbance values recorded for tomato hairy root extracts with the gallic acid calibration curve. The total phenolic content was expressed as &#x03BC;g of gallic acid equivalents (GAE)/g of dry weight. Each analysis consisted of triplicate measurements of each sample and data were averaged over the three measurements.</p>
</sec>
<sec id="S2.SS6">
<title>1,1-Diphenyl-2-Picrylhydrazyl Radical Scavenging Activity Assay</title>
<p>Phenolic compounds accumulating in representative <italic>PhAN4</italic> and GFP-<italic>PhAN4</italic> HRCs were extracted (<xref ref-type="bibr" rid="B133">Morishita et al., 2007</xref>) to apply the DPPH free radical scavenging method in order to establish their antioxidant properties. Ground, freeze-dried tomato HRC (30 mg) were extracted with 0.6 ml EtOH 80% (v/v), shaken in a water bath at 80&#x00B0;C for 40 min, and then centrifuged at 3,000 rpm for 15 min. The recovered supernatant was filtered through polytetrafluoroethylene membrane (0.45 &#x03BC;m) and stored at &#x2212;20&#x00B0;C. The antioxidant capacity of the ethanolic extracts was spectrophotometrically tested by DPPH (1,1-diphenyl-2-picrylhydrazyl) (<xref ref-type="bibr" rid="B103">Li et al., 2010</xref>), with some modifications. Briefly, 0.25 ml of diluted ethanolic extract was added to 2.9 ml of 0.06 mM DPPH working solution. The mixture was shaken and allowed to stand at room temperature, in the dark, for 30 min. Absorbance was measured at 515 nm using a UV-VIS spectrophotometer. Lower absorbance values of the reaction mixture indicated higher free radical scavenging activity. The inhibition of free radical DPPH was expressed as DPPH scavenging effect (% inhibition) I% = {(A0 &#x2212; A1)/A0) &#x00D7; 100}, where A1 and A0 are the absorbance values of blank and of tested samples, respectively. Trolox (vitamin E equivalent antioxidant) was used as the reference standard. Each analysis consisted of triplicate measurements of each sample and data were averaged over the three measurements.</p>
</sec>
<sec id="S2.SS7">
<title>Complementary DNA <italic>L</italic>ibrary <italic>C</italic>onstruction and <italic>S</italic>equencing for <italic>T</italic>ranscriptomic <italic>A</italic>nalysis</title>
<p>Total RNA from wild type and <italic>PhAN4</italic>-1 HRC was extracted using the RNeasy Plant Mini Kit (Qiagen; Valencia, CA, United States). RNA was quantified using the Qubit <sup>&#x00AE;</sup> fluorometer (Thermo Fisher Scientific, Waltham, MA, United States) and assayed through Agilent 2100 Bioanalyzer <sup>&#x00AE;</sup> (Agilent Technologies, Santa Clara, CA, United States) for quality and Integrity Number (RIN) evaluation. Samples with 8 &#x2264; RIN &#x2264; 10 were considered. For each sample, equal amounts of RNA (2 &#x03BC;g) extracted from three biological replicates were pooled for cDNA library construction. First, the poly-A mRNA in the total RNA was pulled down using poly-T oligo-attached magnetic beads. After purification, the mRNA was fragmented at 95&#x00B0;C for 2 min along with RT primer and first-strand buffer. The fragmented RNA was used for the synthesis of the first-strand cDNA by adding DTT, dNTPs, Rnase Inhibitor, and SMARTScribe. All chemicals were incubated for 2 h at 42&#x00B0;C. This was followed by second-strand cDNA synthesis using template-switching oligonucleotide and an additional 1 &#x03BC;l of SMARTScribe. Subsequently, the cDNAs were purified using two rounds of AMPure beads. The samples were enriched by using PCR to create the final library. A final fragment size purification step was performed using the Blue Pippin system selecting fragments between 250 and 500 bp. The libraries were confirmed by electrophoresis on a 1% TAE agarose gel and the Agilent BioAnalyzer 2100 <sup>&#x00AE;</sup> after purification by AMPure bead. The average read size was estimated at 250&#x2013;350 bp. The libraries were sequenced at Novogene Corporation using two lanes of an Illumina HiSeq4000 system with a pair-end run of 2 &#x00D7; 150 bp (Illumina, San Diego, CA, United States).</p>
</sec>
<sec id="S2.SS8">
<title>Sequencing Read Mapping and Identification of Differentially Expressed Genes</title>
<p>Raw RNA-seq libraries were analyzed according to the bioinformatic in-house pipeline (University of Amsterdam, Netherlands)<sup><xref ref-type="fn" rid="footnote1">1</xref></sup>. The raw reads (in FASTQ format) generated from sequencing were cleaned using Trimmomatic version 0.36 (Institut Pasteur, France) (<xref ref-type="bibr" rid="B30">Cock et al., 2009</xref>) by removing adaptor-polluted reads, reads with unknown sequences &#x201C;N&#x201D; accounting for more than 5% and low-quality reads (with a mass value less than 10 and proportion of a total number of bases in the reads greater than 20%). The clean reads were mapped to the <italic>S. lycopersicum</italic> reference genome sequence version ITAG4 (<xref ref-type="bibr" rid="B33">Consortium et al., 2012</xref>) downloaded from the Sol Genomics Network database (<xref ref-type="bibr" rid="B58">Fernandez-Pozo et al., 2015</xref>). Two programs were used for this purpose: Hisat2 version 2.1 (Institut Pasteur, France) (<xref ref-type="bibr" rid="B94">Kim et al., 2015</xref>) and STAR version 2.5.2b (Institut Pasteur, France) (<xref ref-type="bibr" rid="B47">Dobin et al., 2013</xref>). The mapping results were compared with the Picard Tools CollectAlignmentSummaryMetrics version 1.138 (Broad Institute, Cambridge, MA, United States)<sup><xref ref-type="fn" rid="footnote2">2</xref></sup>. The STAR mapping results were selected for further analysis. BAM files were transformed to a subread matrix file using the Rsubread version 1.34.4 R package (Bioconductor, open source) (<xref ref-type="bibr" rid="B111">Liao et al., 2019</xref>). Differential expression analysis was performed with the DESeq2 R package version 1.22.2 (Bioconductor, open source) (<xref ref-type="bibr" rid="B119">Love et al., 2014</xref>). Genes with an adjusted <italic>P</italic>-value of &#x2264;0.001 and a log2 fold change of &#x2265;2 were defined as differentially expressed (<xref ref-type="bibr" rid="B14">Benjamini and Hochberg, 1995</xref>).</p>
</sec>
<sec id="S2.SS9">
<title>Functional Annotation and Enrichment Pathway Analysis of Differentially Expressed Genes and Identification of Tomato Genes</title>
<p>The list of DEGs (Cluster 1 &#x2013; <italic>PhAN4</italic>/WT &#x003C; 1 and Cluster 2 &#x2013; <italic>PhAN4</italic>/WT &#x003E; 1) was analyzed using the g:Profiler (<xref ref-type="bibr" rid="B154">Reimand et al., 2007</xref>) with the default parameters using Organism <italic>Solanum lycopersicum</italic>. No terms were statistically significant under the &#x201C;Measure underrepresentation&#x201D; option. The results were exported as CSV and uploaded into R Studio where they were plotted with ggplot2<sup><xref ref-type="fn" rid="footnote3">3</xref></sup>. The gene functional annotation was performed by sequence homology search with different protein data sets using BLASTP and Protein domains search using InterPro Scan.</p>
</sec>
<sec id="S2.SS10">
<title>Measurements of Tomato Hairy Root Cultures pH</title>
<p>Measurement of both control and PhAN4 HRCs pH was accomplished as described by <xref ref-type="bibr" rid="B197">Verweij et al. (2008)</xref>. Briefly, 10 mg of hairy root material were ground in 2 ml distilled water and immediately measured with a pH electrode (edge <sup>&#x00AE;</sup> Multiparameter pH Meter &#x2013; Hanna Instruments, Italy).</p>
</sec>
<sec id="S2.SS11">
<title>Gamma Irradiation Tests</title>
<p>Irradiation tests were performed at the Calliope facility, a pool-type irradiation plant equipped with a <sup>60</sup>Co gamma source in a high volume (7 m &#x00D7; 6 m &#x00D7; 3.9 m) shielded cell at ENEA (Casaccia Research Centre, Rome, Italy). The source emits radiations consisting of two gamma photons with a mean energy of 1.25 MeV (<xref ref-type="bibr" rid="B12">Baccaro et al., 2019</xref>). Fricke dosimetric system was employed for the determination of the absorbed dose during the irradiation tests. HRCs-derived samples were irradiated at room temperature, at three different absorbed doses (0.5, 1, and 2 kGy), and a dose rate of 1.8 kGywater/h.</p>
</sec>
<sec id="S2.SS12">
<title>Electron Spin Resonance Spectroscopy Before and After Gamma Irradiation</title>
<p>The molecular species accumulating upon the ectopic expression of <italic>PhAN4</italic> were investigated for possible efficient maintenance of the ability to counteract the generation of reactive oxygen species upon strong ROS inducers such as ionizing radiations. Gamma rays were used to generate peroxyl radicals (which are proportional to the number of paramagnetic species present in the samples) in lyophilized HRC powder. We explored ROS formation before and after 0.5, 1, and 2 kGy absorbed dose in AN4-1 and control HRCs sample sets by ESR Spectroscopy measurements. Not irradiated sample sets were used as references. Each set consisted of two replicates. For each ESR analysis, 8 &#x00B1; 0.1 mg of HRC lyophilized powder was split into two PT-Capillaries (NOX-A.8.1-PT NOXYGEN, Holland) that were then inserted in a conventional quartz sample tube (o.d./i.d. of 4/3 mm) closed by a plastic lid. Irradiated samples were analyzed straight after the end of irradiation and ESR signals and were normalized to the sample mass. ESR measurements were acquired using an ESR e-scan spectrometer (Bruker, Billerica, MA, United States) operating in the X-band frequency (9.4 GHz) with a field modulation frequency of 86 kHz and modulation amplitude of 5.152 G. The ESR spectra were recorded at a central magnetic field of 3466 Gauss with a sweep width of 160 G, microwave power of 0.14 mW, microwave frequency of 9.75 GHz. The ESR spectra reported in this work derived from the accumulation of four scans. Bruker WinEPR data processing software (Bruker, Billerica, MA, United States) was used for data elaboration.</p>
</sec>
<sec id="S2.SS13">
<title>Ultraviolet-Visible Absorbance Spectra Analysis Before and After Gamma Irradiation</title>
<p>Ultraviolet-visible (UV-VIS) spectra were obtained from crude extracts of AN4-1 and control HRCs. Briefly, lyophilized HRCs were ground in liquid nitrogen and the resulting powder was finely homogenized using an Ultraturrax homogenizer (IKA, Germany) in water:HCl (100:1, v/v). Samples were incubated at 500 rpm for 1 h at R.T., clarified by centrifugation at 11,000 &#x00D7; <italic>g</italic> for 30 min. The resulting supernatants were examined at 280&#x2013;600 nm, by a UV-spectrophotometer (Lambda 950, Perkin Elmer, Waltham, MA, United States) at R.T. with a slit width of 2 nm, using a 10 mm cell.</p>
</sec>
<sec id="S2.SS14">
<title>Photoluminescence Analysis Before and After Gamma Irradiation</title>
<p>Samples were finely ground in liquid nitrogen with mortar and pestle, resuspended, and homogenized in phosphate-buffered saline pH 7.2 (PBS, 1:3 w/v) containing a protease inhibitor cocktail (Complete&#x2122;; Roche, Mannheim, Germany) to extract soluble proteins. Photoluminescence emission spectra of extracts were determined before and straight after 2 kGy absorbed dose in AN4-1 and control HRC dried biomass sample sets. Two replicates per set were poured into quartz cuvettes with an optical path length of 1 cm (104F-QS, Hellma, Germany). The emission spectra were recorded using the Edinburgh Instruments FS 5 spectrometer in the range 300&#x2013;800 nm with 280 nm excitation wavelength. The recorded spectra were mass-normalized and corrected for background scattering (reference: extraction buffer).</p>
</sec>
<sec id="S2.SS15">
<title>Statistical Analysis</title>
<p>All data (HRCs growth, <italic>PhAN4</italic> gene expression, total phenolic content, DPPH antioxidant capacity, total anthocyanin content) were subjected to one-way ANOVA with Tukey&#x2019;s post-test to determine the differences in average of all tested parameters &#x00B1; <italic>SD</italic>. A <italic>p</italic>-value less than 0.05 was considered statistically significant. GraphPad Prism version 8.0.2 for Windows (GraphPad Software, San Diego, CA, United States) was used for graphical and statistical data processing.</p>
</sec>
</sec>
<sec sec-type="results" id="S3">
<title>Results</title>
<sec id="S3.SS1">
<title>Hairy Roots Generation and Screening</title>
<p>Both 35S:<italic>PhAN4</italic> and 35S:GFP-<italic>PhAN4</italic> constructs were independently transferred into the miniature tomato genotype MicroTom to generate hairy root cultures. Control HRCs were obtained by transformation with <italic>A. rhizogenes</italic> not containing <italic>PhAN4</italic>. HRCs were collected from independent explants. While control HRCs grew as unpigmented organ cultures (<xref ref-type="fig" rid="F1">Figure 1A</xref>, left), HRCs generated by 35S:<italic>PhAN4</italic> and 35S:GFP-<italic>PhAN4</italic> showed purple pigmentation (<xref ref-type="fig" rid="F1">Figure 1A</xref>, right) that may vary among clones. Purple pigmentation was present on primary and secondary branches and was maintained on kanamycin selection (<xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 1</xref>). HRCs showed typical abundant secondary branching. Three clones for each construct were selected and further analyzed. No statistical difference was found in the growth rate of PhAN4, GFP-PhAN4, and control HRCs (<xref ref-type="fig" rid="F1">Figure 1B</xref>).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption><p>Control (left) and transformed (35S:AN4, right) MicroTom hairy roots <bold>(A)</bold>. Hairy root culture (HRC) growth estimation by an increase in fresh weight along 28 days of cultures in MS medium (one-way ANOVA analysis of variance with Tukey&#x2019;s <italic>post-hoc</italic> test) by GraphPad Prism <bold>(B)</bold>.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g001.tif"/>
</fig>
<p>Polymerase chain reaction (PCR) screening showed amplification of the expected fragments from genomic DNA, confirming integration of the necessary root-inducing genes from <italic>A. rhizogenes</italic> and of the <italic>PhAN4</italic> transgene (<xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 2A</xref>). No transgene loss was observed over time (<xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 2B</xref>). Control HRCs were negative for <italic>PhAN4</italic> amplification, as expected. Integration of <italic>PhAN4</italic> was estimated at copy numbers ranging from 4 to 8 copies, depending on the selected clone analyzed (<xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 3</xref>). <italic>PhAN4</italic> transcripts were detected in both HRCs harboring either 35S:<italic>PhAN4</italic> or 35S:GFP-<italic>PhAN4</italic> constructs, while they were absent in the control, as expected (<xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 3</xref>).</p>
</sec>
<sec id="S3.SS2">
<title>Liquid Chromatography Coupled to High-Resolution Mass Spectrometry Analysis of Phenylpropanoids</title>
<p>Total anthocyanins content was measured. AN4-1 and AN4-4 HRCs showed the highest anthocyanins concentrations, equal to 37 and 36.6 &#x03BC;g/g<sub>dried weight</sub> (<xref ref-type="fig" rid="F2">Figure 2A</xref>), respectively. The anthocyanins profile was determined by LC-HRMS and compared to control HRCs. Identification was achieved by m/z ion reconstruction starting with the aglycon (delphinidin, petunidin, pelargonidin, malvidin), followed by the recognition of all the conjugated sugar and phenolic moieties. Subsequently, absolute quantification was performed as previously described (<xref ref-type="bibr" rid="B46">Diretto et al., 2019</xref>; <xref ref-type="bibr" rid="B29">Carmona et al., 2021</xref>) and by interpolating anthocyanin signal intensities in the roots compared to the ones of external calibration curves of the Pelargonidin-3-glucoside and Delphinidin 3,5-<italic>O</italic>-diglucoside standards. In our experimental conditions, anthocyanins were virtually undetectable in control HRCs. Petunidin-3-(p-coumaroyl)-rutinoside-5-glucoside1 and Delphinidin 3,5-<italic>O</italic>-diglucoside were the most abundant anthocyanins in the <italic>PhAN4</italic> roots, followed by a second group including Petunidin-3-(p-coumaroyl)-rutinoside-5-glucoside2, Petunidin-3-feruloyl-rutinoside-5-glucoside and Delphinidin-3-(p-coumaroyl)-rutinoside-5-glucoside. Two additional anthocyanins, Pelargonidin-3-glucoside and Malvidin-3-<italic>O</italic>-(4&#x201D;&#x2019;coumaroyl)-rutinose-5-<italic>O</italic>-glucose, were detected, although at low levels (<xref ref-type="fig" rid="F2">Figure 2B</xref>; <xref ref-type="bibr" rid="B177">Su et al., 2016</xref>). All lines show about the same relative amount of the different anthocyanin species.</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption><p>Anthocyanins in PhAN4 HRC clones. Total anthocyanins content <bold>(A)</bold> and amount of specific anthocyanins <bold>(B)</bold> of six representative PhAN4-expressing hairy root clones. Columns report average values &#x00B1; <italic>SD</italic> (<italic>n</italic> = 3).</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g002.tif"/>
</fig>
<p>To evaluate the effect of the accumulation of anthocyanins on their precursors and the final balance on flavonoids accumulation, a detailed analysis of phenylpropanoids was carried out by LC-HRMS on the engineered HRCs. A graphical representation of the accumulation levels of anthocyanins precursors is shown for the best anthocyanin-accumulating AN4-1 HRC (<xref ref-type="fig" rid="F3">Figures 3</xref>, <xref ref-type="fig" rid="F4">4</xref>) and the other engineered HRC (<xref ref-type="supplementary-material" rid="FS1">Supplementary Files 1</xref>, <xref ref-type="supplementary-material" rid="FS2">2</xref>). A series of phenolic acids and their derivatives (e.g., dicaffeoylquinic, 5-caffeoyl-quinic, and 4-caffeoyl-quinic acids) were accumulated at a significantly lower level compared to control. This finding might be ascribed to the role of these compounds as flavanones and flavonols precursors of their sugar-decorated derivatives and of anthocyanins that, in turn, resulted to be enhanced in accumulation in engineered HRCs. As a consequence of the lower accumulation of phenolic acids, hydroxycinnamic acid accumulated at reduced levels in engineered HRCs, with respect to control. Interestingly, the hydroxybenzoic acid level was not significantly different. Significantly higher levels of other valuable phenolics such as coumaric acid and caffeic acid derivatives were found in AN4-1 HRC compared to control (<xref ref-type="fig" rid="F3">Figure 3</xref>).</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption><p>Graph representing phenolic compounds and their derivatives expressed as internal standard (formononetin) fold of control and AN4-1 HRCs. Columns report average values &#x00B1; <italic>SD</italic> (<italic>n</italic> = 3). &#x002A;<italic>p</italic>-value &#x2264; 0.05, &#x002A;&#x002A;<italic>p</italic>-value &#x2264; 0.01 and &#x002A;&#x002A;&#x002A;<italic>p</italic>-value &#x2264; 0.001.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g003.tif"/>
</fig>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption><p>Flavonoids are expressed as internal standard (formononetin) fold of control and AN4-1 HRCs. Columns report average values &#x00B1; <italic>SD</italic> (<italic>n</italic> = 3). &#x002A;<italic>p</italic>-value &#x2264; 0.05, &#x002A;&#x002A;<italic>p</italic>-value &#x2264; 0.01 and &#x002A;&#x002A;&#x002A;<italic>p</italic>-value &#x2264; 0.001.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g004.tif"/>
</fig>
<p>Accordingly, among flavonoids, both flavanones (i.e., naringenin chalcone and its sugar-decorated derivatives, naringenin, eriodictyol) and flavonols (i.e., dihydrokaempferol, sugar-decorated kaempferol, dihydroquercetin, quercetin derivatives, rutin, and myricetin) resulted in an overall significantly higher accumulation in engineered HRCs compared to control (<xref ref-type="fig" rid="F4">Figure 4</xref> and <xref ref-type="supplementary-material" rid="FS2">Supplementary File 2</xref>). Notably, and coherently with phenolic acids precursor function, the observed fold change levels on most flavonoid groups (from naringenin and kaempferol derivatives to quercetin derivatives and rutin) displayed a much larger extent (192.82 &#x00B1; 39.1 for naringenin dihexose I) compared to the phenolic acid precursor (0.623 &#x00B1; 0.069 for 4-caffeoyl-quinic acids).</p>
<p>AN4-1 HRC was chosen as the candidate to perform the subsequent transcriptome analysis due to the higher content of the different anthocyanin and flavonoid species compared to the remaining clones.</p>
</sec>
<sec id="S3.SS3">
<title>Transcriptome Analysis of Tomato <italic>PhAN4</italic> Hairy Roots</title>
<p>The response to the constitutive expression of <italic>PhAN4</italic> in tomato HRCs were analyzed transcriptome-wide by RNAseq analysis and compared to control HRCs. AN4-1 showed a total of 442 differentially expressed genes (DEGs), of which 331 were upregulated and 111 were downregulated (<xref ref-type="table" rid="T1">Table 1</xref> and <xref ref-type="supplementary-material" rid="FS3">Supplementary File 3</xref>). After Gene Ontology Enrichment (GOE) analysis, 38 upregulated and 8 downregulated genes were termed (<xref ref-type="supplementary-material" rid="FS4">Supplementary File 4</xref>). For upregulated DEGs, 3 GO categories were assigned: Molecular Function (MF), Biological Process (BP), and Cellular Component (CC) (<xref ref-type="fig" rid="F5">Figure 5</xref>).</p>
<table-wrap position="float" id="T1">
<label>TABLE 1</label>
<caption><p>List of the more representative and significant DEGs obtained from the GOE and functional annotation analyses in relation to agrospace application.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Gene ID</td>
<td valign="top" align="center">Log<sub>2</sub>Fc</td>
<td valign="top" align="center">Gene name</td>
<td valign="top" align="left">Function</td>
<td valign="top" align="left">References</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Solyc03g020080.3.1</td>
<td valign="top" align="center">2.017930333</td>
<td valign="top" align="center"><italic>SlPI11</italic></td>
<td valign="top" align="left">Pin-II type proteinase inhibitor/<bold>biotic (herbivorous and insects resistance), abiotic (drought/heat)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B52">Fan et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc03g020030.3.1</td>
<td valign="top" align="center">10.72904412</td>
<td valign="top" align="center"><italic>SlPI16</italic></td>
<td valign="top" align="left">Pin-II type proteinase inhibitor/<bold>biotic (wound stress, insect resistance), abiotic (heat)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B52">Fan et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc11g020960.2.1</td>
<td valign="top" align="center">2.362943887</td>
<td valign="top" align="center"><italic>SlPI51</italic></td>
<td valign="top" align="left">Proteinase inhibitor II/<bold>biotic (wound stress)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B52">Fan et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc08g080630.3.1</td>
<td valign="top" align="center">2.33279266</td>
<td valign="top" align="center"><italic>SlPI31</italic></td>
<td valign="top" align="left">Proteinase inhibitor 1/<bold>biotic (TSWV infection), abiotic (drought)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B52">Fan et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g086090.2.1</td>
<td valign="top" align="center">2.247200225</td>
<td valign="top" align="center"><italic>SlPI47</italic></td>
<td valign="top" align="left">Trypsin inhibitor 1/<bold>abiotic (drought)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B52">Fan et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g086100.2.1</td>
<td valign="top" align="center">2.406338004</td>
<td valign="top" align="center"><italic>SlPI48</italic></td>
<td valign="top" align="left">Proteinase inhibitor/<bold>abiotic (heat)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B52">Fan et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g059965.1.1</td>
<td valign="top" align="center">3.476158885</td>
<td valign="top" align="center"><italic>SlGluB</italic></td>
<td valign="top" align="left">Beta-1,3-glucanase/<bold>biotic (defense against pathogens: <italic>C. fulvum</italic>, <italic>P. infestans</italic>)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B193">van Kan et al., 1992</xref>; <xref ref-type="bibr" rid="B51">Fan et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g091510.3.1</td>
<td valign="top" align="center">12.25514456</td>
<td valign="top" align="center"><italic>CHS</italic></td>
<td valign="top" align="left">Chalcone synthase 1/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B212">Zhang et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc05g053550.3.1</td>
<td valign="top" align="center">9.83030415</td>
<td valign="top" align="center"><italic>CHS</italic></td>
<td valign="top" align="left">Chalcone synthase 2/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B89">Kalt et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g083860.3.1</td>
<td valign="top" align="center">6.299607501</td>
<td valign="top" align="center"><italic>F3H</italic></td>
<td valign="top" align="left">Flavonoid-3-hydroxylase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B9">Aoki et al., 2010</xref>; <xref ref-type="bibr" rid="B212">Zhang et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g085020.3.1</td>
<td valign="top" align="center">10.09460014</td>
<td valign="top" align="center"><italic>DFR</italic></td>
<td valign="top" align="left">Dihydroflavonol reductase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B20">Bongue-Bartelsman et al., 1994</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g106650.3.1</td>
<td valign="top" align="center">3.003680242</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Xyloglucan endotransglucosylase/<bold>cell elongation</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B109">Li P. et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc11g011210.2.1</td>
<td valign="top" align="center">2.189943987</td>
<td valign="top" align="center"><italic>RSI-1</italic></td>
<td valign="top" align="left">RSI-1 precursor/<bold>lateral root initiation</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B183">Taylor and Scheuring, 1994</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc03g093390.3.1</td>
<td valign="top" align="center">2.390710296</td>
<td valign="top" align="center"><italic>LeEXPB2</italic></td>
<td valign="top" align="left">Expansin-B15-like/<bold>sexual reproduction</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B181">Sundaresan et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc08g077910.3.1</td>
<td valign="top" align="center">3.227703527</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Expansin-like B1/<bold>sexual reproduction</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B137">Nveawiah-Yoho et al., 2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc05g052245.1.1</td>
<td valign="top" align="center">2.186779111</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Expansin A8-like/<bold>cell wall organization</bold></td>
<td valign="top" align="left">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g010860.3.1</td>
<td valign="top" align="center">2.630126243</td>
<td valign="top" align="center"><italic>EXPA4</italic></td>
<td valign="top" align="left">Expansin 4-like/<bold>cell wall organization</bold></td>
<td valign="top" align="left">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g062510.3.1</td>
<td valign="top" align="center">2.392338587</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Peroxidase 72-like/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B137">Nveawiah-Yoho et al., 2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc04g080760.3.1</td>
<td valign="top" align="center">2.42913063</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Peroxidase 9/<bold>abiotic stress (hypoxia tolerance)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B8">Andolfo et al., 2014</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g077300.2.1</td>
<td valign="top" align="center">7.236518572</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Peroxidase 19/<bold>phenylpropanoids biosynthesis, biotic (ToMV infection)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B8">Andolfo et al., 2014</xref>; <xref ref-type="bibr" rid="B160">Safavi-Rizi et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc06g054320.1.1</td>
<td valign="top" align="center">2.690758759</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Dirigent protein/<bold>lignin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B142">Paniagua et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g055190.1.1</td>
<td valign="top" align="center">5.216357243</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Dirigent protein/<bold>lignin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B142">Paniagua et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g055200.1.1</td>
<td valign="top" align="center">2.06850204</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Dirigent protein/<bold>lignin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B142">Paniagua et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc04g010270.1.1</td>
<td valign="top" align="center">2.350516375</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Dirigent protein/<bold>lignin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B142">Paniagua et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g076710.3.1</td>
<td valign="top" align="center">2.307987898</td>
<td valign="top" align="center"><italic>CathB</italic></td>
<td valign="top" align="left">Cathepsin B-like cysteine/<bold>biotic (hypersensitive response)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B127">McLellan et al., 2009</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc05g053890.2.1</td>
<td valign="top" align="center">&#x2212;2.032569214</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">UDP-GT-like/<bold>flavonoids glycosylation</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B57">Fernandez-Moreno et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g096560.2.1</td>
<td valign="top" align="center">4.109312617</td>
<td valign="top" align="center"><italic>TomLOXD</italic></td>
<td valign="top" align="left">Subtilisin-like protease/<bold>biotic (wound stress, resistance to insects and necrotrophic pathogens)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B206">Yan et al., 2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc07g054840.3.1</td>
<td valign="top" align="center">3.341226163</td>
<td valign="top" align="center"><italic>AtMYB41</italic></td>
<td valign="top" align="left">Transcription factor 41/<bold>abiotic (salt tolerance)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B79">Hoang et al., 2012</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc03g095810.3.1</td>
<td valign="top" align="center">6.923791313</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Trichome birefringence-like/<bold>xylan acetylation (resistance against micro-organisms, cold and drought)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B216">Zhang et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g007970.2.1</td>
<td valign="top" align="center">6.961895177</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Transcription factor 77/<bold>abiotic (water deficit)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B10">Asins et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc07g043690.2.1</td>
<td valign="top" align="center">2.800732902</td>
<td valign="top" align="center"><italic>SlNPR1</italic></td>
<td valign="top" align="left">3-Hydroxyisobutyryl-CoA hydrolase/<bold>abiotic (drought stress)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B105">Li J. et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc03g096460.3.1</td>
<td valign="top" align="center">2.302142017</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left"><bold>Wound signaling</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B167">Scranton et al., 2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g080790.3.1</td>
<td valign="top" align="center">3.317661852</td>
<td valign="top" align="center"><italic>SlDHS</italic></td>
<td valign="top" align="left">Deoxyhypusine synthase/osmotic stress and chilling injury</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B202">Wang et al., 2001</xref>; <xref ref-type="bibr" rid="B72">Gupta et al., 2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g081300.1.1</td>
<td valign="top" align="center">2.564715</td>
<td valign="top" align="center"><italic>SlMC8</italic></td>
<td valign="top" align="left">Metacaspase 9/<bold>biotic (apoptosis induction by pests), abiotic (drought, cold and salt)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B112">Liu et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g080690.2.1</td>
<td valign="top" align="center">2.304387313</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Patatin/<bold>abiotic (flooding)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B39">de Ollas et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc06g073760.3.1</td>
<td valign="top" align="center">4.071580028</td>
<td valign="top" align="center"><italic>BGL2</italic></td>
<td valign="top" align="left">Beta-glucosidase/<bold>sugar/organic acid ratio tomato fruits/resistance against different pathogens/softening</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B112">Liu et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g035225.1.1</td>
<td valign="top" align="center">9.263765052</td>
<td valign="top" align="center"><italic>RICESLEEPER1</italic></td>
<td valign="top" align="left">BED zinc-finger/<bold>abiotic (salt tolerance)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B90">Kashyap et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g010500.2.1</td>
<td valign="top" align="center">5.358159809</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">E3 ubiquitin protein/<bold>biotic (resistance to <italic>X. perforans</italic>)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g010670.1.1</td>
<td valign="top" align="center">5.364030417</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">E3 ubiquitin protein/<bold>biotic (resistance to <italic>X. perforans</italic>)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g009630.2.1</td>
<td valign="top" align="center">5.183567126</td>
<td valign="top" align="center"><italic>SlCaM3</italic></td>
<td valign="top" align="left">Calcium-binding protein/<bold>biotic (<italic>B. cinerea</italic>), abiotic (mechanical wounding, salt and cold stress)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B144">Peng et al., 2014</xref>; <xref ref-type="bibr" rid="B172">Shi and Du, 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g067750.3.1</td>
<td valign="top" align="center">6.915338794</td>
<td valign="top" align="center"><italic>CA1</italic></td>
<td valign="top" align="left">Carbonic anhydrase/<bold>abiotic (drought stress)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B110">Li X. et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc08g075705.1.1</td>
<td valign="top" align="center">4.258074963</td>
<td valign="top" align="center"><italic>pTRX y2</italic></td>
<td valign="top" align="left">Thioredoxin Y2/<bold>ROS detoxification, redox signaling network regulation</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B169">Serrato et al., 2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g007190.3.1</td>
<td valign="top" align="center">&#x2212;2.218315202</td>
<td valign="top" align="center"><italic>PRXL2A</italic></td>
<td valign="top" align="left">Peroxiredoxin-like 2A/<bold>redox regulatory protein</bold></td>
<td valign="top" align="left">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Solyc03g098760.2.1</td>
<td valign="top" align="center">&#x2212;5.109469505</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">I3 Kunitz-type trypsin inhibitor/<bold>biotic (infection <italic>Tetranychus</italic> species infection)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B87">Islam et al., 2015</xref>; <xref ref-type="bibr" rid="B164">Schimmel et al., 2018</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g089490.3.1</td>
<td valign="top" align="center">&#x2212;5.211378167</td>
<td valign="top" align="center"><italic>SlPI40</italic></td>
<td valign="top" align="left">Proteinase inhibitor/<bold>abiotic (drought, salt) biotic (<italic>B. cinerea</italic>, TSWV infection)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B52">Fan et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc06g008760.1.1</td>
<td valign="top" align="center">&#x2212;3.056115855</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Glutaredoxin-C13-like/<bold>upregulated in tomato <italic>rin</italic> mutants</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B100">Kumar et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc07g055610.2.1</td>
<td valign="top" align="center">&#x2212;2.055605009</td>
<td valign="top" align="center"><italic>PR1</italic></td>
<td valign="top" align="left">Resistance protein R1/<bold>biotic (resistance to late blight and <italic>F. oxysporum</italic> infection)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B21">Bournival et al., 1989</xref>; <xref ref-type="bibr" rid="B140">Pan et al., 2000</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g010480.3.1</td>
<td valign="top" align="center">&#x2212;2.123574853</td>
<td valign="top" align="center"><italic>KAT1</italic></td>
<td valign="top" align="left">K+ channel KAT1/<bold>abiotic (tolerance to potassium deficiency)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B217">Zhao et al., 2018</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g102610.3.1</td>
<td valign="top" align="center">&#x2212;3.607916378</td>
<td valign="top" align="center"><italic>FRO6</italic></td>
<td valign="top" align="left">Ferric reduction oxidase 6/<bold>biotic (<italic>P. solani</italic> infection)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B25">Buoso et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc05g010320.3.1</td>
<td valign="top" align="center">4.308610241</td>
<td valign="top" align="center"><italic>CHI</italic></td>
<td valign="top" align="left">Chalcone isomerase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B134">Morita et al., 2014</xref>; <xref ref-type="bibr" rid="B106">Li Z. et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc05g052240.3.1</td>
<td valign="top" align="center">8.452278685</td>
<td valign="top" align="center"><italic>CHI</italic></td>
<td valign="top" align="left">Chalcone isomerase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B157">Ron et al., 2014</xref>; <xref ref-type="bibr" rid="B80">Hou et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc11g066580.2.1</td>
<td valign="top" align="center">16.35234434</td>
<td valign="top" align="center"><italic>F3&#x2032;5&#x2032;H</italic></td>
<td valign="top" align="left">Flavonoid-3&#x2032;,5&#x2032;-hydroxylase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc08g080040.3.1</td>
<td valign="top" align="center">8.861102345</td>
<td valign="top" align="center"><italic>ANS</italic></td>
<td valign="top" align="left">Anthocyanin synthase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc04g078140.3.1</td>
<td valign="top" align="center">8.35041607</td>
<td valign="top" align="center"><italic>DilFl</italic></td>
<td valign="top" align="left">Cytochrome B5/<bold>phenylpropanoids biosynthesis (essential for full activity of F3&#x2032;5&#x2032;H)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B41">de Vetten et al., 1999</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g082660.3.1</td>
<td valign="top" align="center">15.05027118</td>
<td valign="top" align="center"><italic>OMT</italic></td>
<td valign="top" align="left">Caffeoyl-CoA-<italic>O</italic>-methyltransferase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B156">Roldan et al., 2014</xref>; <xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g062975.1.1</td>
<td valign="top" align="center">7.081891304</td>
<td valign="top" align="center"><italic>3UFGT</italic></td>
<td valign="top" align="left">UDP-glucose flavonoid 3-<italic>O</italic>-glucosyl transferases/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B81">Hu et al., 2011</xref>; <xref ref-type="bibr" rid="B188">Tohge et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g083440.1.1</td>
<td valign="top" align="center">9.972475187</td>
<td valign="top" align="center"><italic>3UFGT</italic></td>
<td valign="top" align="left">UDP-glucose flavonoid 3-<italic>O</italic>-glucosyl transferases/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B81">Hu et al., 2011</xref>; <xref ref-type="bibr" rid="B187">Tohge et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g098590.2.1</td>
<td valign="top" align="center">16.55105848</td>
<td valign="top" align="center"><italic>3UFGT</italic></td>
<td valign="top" align="left">UDP-glucose flavonoid 3-<italic>O</italic>-glucosyl transferases/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B81">Hu et al., 2011</xref>; <xref ref-type="bibr" rid="B188">Tohge et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g059170.2.1</td>
<td valign="top" align="center">8.326262972</td>
<td valign="top" align="center"><italic>3RT</italic></td>
<td valign="top" align="left">Anthocyanidin-3-<italic>O</italic>-glucoside rhamnosyltransferase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B188">Tohge et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g088170.2.1</td>
<td valign="top" align="center">13.21347105</td>
<td valign="top" align="center"><italic>AAT</italic></td>
<td valign="top" align="left">Flavonoid-3-<italic>O</italic>-rutinoside-4&#x201D;&#x2019;-<italic>O</italic>-phenylacyltransferase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B60">Florio et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc03g025190.4.1</td>
<td valign="top" align="center">16.80814437</td>
<td valign="top" align="center"><italic>MTP77</italic></td>
<td valign="top" align="left">Transparent testa 2-like/<bold>toxic compound extrusion, regulation of cell turgescence</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B48">dos Santos et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g006120.2.1</td>
<td valign="top" align="center">7.357873128</td>
<td valign="top" align="center"><italic>LDOX</italic></td>
<td valign="top" align="left">Leucoanthocyanidin dioxygenase/<bold>phenylpropanoids biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B143">Pelletier et al., 1997</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc07g052490.3.1</td>
<td valign="top" align="center">7.173073383</td>
<td valign="top" align="center"><italic>Atv</italic></td>
<td valign="top" align="left">Myb-like transcription factor Atv/<bold>anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B28">Cao et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g086290.2.1</td>
<td valign="top" align="center">8.651275639</td>
<td valign="top" align="center"><italic>SlAN2</italic></td>
<td valign="top" align="left">AN2-like transcription factor/<bold>anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B179">Sun C. et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g005800.2.1</td>
<td valign="top" align="center">7.517786731</td>
<td valign="top" align="center"><italic>SlMYBATV-like</italic></td>
<td valign="top" align="left">R3-MYB repressor/<bold>anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B28">Cao et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g065100.2.1</td>
<td valign="top" align="center">14.18672027</td>
<td valign="top" align="center"><italic>AN1</italic></td>
<td valign="top" align="left">AN1-like transcription factor/<bold>anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B152">Qiu et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g084380.1.1</td>
<td valign="top" align="center">3.439413134</td>
<td valign="top" align="center"><italic>PH3</italic></td>
<td valign="top" align="left">WRKY transcription factor/<bold>anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B198">Verweij et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc10g083900.2.1</td>
<td valign="top" align="center">3.542474125</td>
<td valign="top" align="center"><italic>Myb27</italic></td>
<td valign="top" align="left">MYB transcription factor/<bold>inhibitor of anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B2">Albert et al., 2011</xref>, <xref ref-type="bibr" rid="B1">2014</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g095640.2.1</td>
<td valign="top" align="center">4.928760848</td>
<td valign="top" align="center"><italic>SlTRY</italic></td>
<td valign="top" align="left">Trichome initiation factor ECT3/<bold>anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B189">Tominaga-Wada et al., 2013</xref>; <xref ref-type="bibr" rid="B95">Kim et al., 2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g105880.4.1</td>
<td valign="top" align="center">3.469067651</td>
<td valign="top" align="center"><italic>TPS4</italic></td>
<td valign="top" align="left">Monoterpenoid synthase/<bold>terpene biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B196">Vel&#x00E1;zquez-M&#x00E1;rquez et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g092470.2.1</td>
<td valign="top" align="center">5.695783056</td>
<td valign="top" align="center"><italic>TPS14</italic></td>
<td valign="top" align="left">Sesquiterpene synthase/<bold>terpene biosynthesis, biotic (<italic>F. oxysporum</italic> resistance)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B196">Vel&#x00E1;zquez-M&#x00E1;rquez et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc11g017240.2.1</td>
<td valign="top" align="center">3.78371117</td>
<td valign="top" align="center"><italic>SlCM2</italic></td>
<td valign="top" align="left">Chorismate mutase/<bold>volatile compounds biosynthesis, abiotic (drought stress)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B191">Tzin et al., 2015</xref>; <xref ref-type="bibr" rid="B59">Filiz et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc08g008630.3.1</td>
<td valign="top" align="center">&#x2212;3.340796451</td>
<td valign="top" align="center"><italic>Dwarf27</italic></td>
<td valign="top" align="left">Beta-carotene isomerase D27/<bold>strigolactone and beta-carotene biosynthesis, biotic (psyllid resistance)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B76">Harrison et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc04g050930.3.1</td>
<td valign="top" align="center">&#x2212;2.072953851</td>
<td valign="top" align="center"><italic>VDE</italic></td>
<td valign="top" align="left">Violaxanthin de-epoxidase VDE/<bold>carotenoid biosynthesis, biotic (<italic>P. syringae</italic> infection), abiotic (anoxia)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B209">Yang Y. X. et al., 2015</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc05g010180.3.1</td>
<td valign="top" align="center">&#x2212;2.221215961</td>
<td valign="top" align="center"><italic>CRTISO</italic></td>
<td valign="top" align="left">Carotenoid isomerase/<bold>carotenoid biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B86">Isaacson et al., 2002</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g006140.2.1</td>
<td valign="top" align="center">4.364619823</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Chlorophyll a/b-binding protein/<bold>fruits ripening</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B219">Zouari et al., 2014</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g065220.3.1</td>
<td valign="top" align="center">&#x2212;2.141082227</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Cytochrome P450/<bold>fruits ripening (extended shelf-life</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B64">Gao et al., 2018</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc09g066150.1.1</td>
<td valign="top" align="center">&#x2212;4.574546484</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Cytochrome P450/<bold>fruits ripening (extended shelf-life)</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B64">Gao et al., 2018</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc07g006570.3.1</td>
<td valign="top" align="center">4.221848981</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Ribonuclease 3-like/<bold>RNA biogenesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B33">Consortium et al., 2012</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g065230.3.1</td>
<td valign="top" align="center">3.170387722</td>
<td valign="top" align="center"><italic>IMT7</italic></td>
<td valign="top" align="left">Cytochrome P450</td>
<td valign="top" align="left">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g091440.2.1</td>
<td valign="top" align="center">2.129583909</td>
<td valign="top" align="center"><italic>bHLH83-like</italic></td>
<td valign="top" align="left">bHLH/<bold>enhance root hair initiation, promote flowering in short day and maintain the iron balance</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B151">Qian et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g088130.2.1</td>
<td valign="top" align="center">4.327213562</td>
<td valign="top" align="center"><italic>bHLH93-like</italic></td>
<td valign="top" align="left">bHLH/<bold>enhance root hair initiation, promote flowering in short day</bold></td>
<td valign="top" align="left">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Solyc04g077780.3.1</td>
<td valign="top" align="center">2.019567752</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">LIM transcription factor/<bold>cytoskeleton organization</bold></td>
<td valign="top" align="left">&#x2013;</td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g013850.2.1</td>
<td valign="top" align="center">&#x2212;2.036803744</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Glycosyltransferase/<bold>regulates anther development and male-sterility</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B138">Omidvar et al., 2015</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc02g081340.3.1</td>
<td valign="top" align="center">10.53476424</td>
<td valign="top" align="center"><italic>GST</italic></td>
<td valign="top" align="left">Glutathione-<italic>S</italic>-transferase/<bold>anthocyanin biosynthesis</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B4">Alfenito et al., 1998</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc01g058030.2.1</td>
<td valign="top" align="center">8.08401203</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Gibberellin 2-beta-dioxygenase/<bold>determines dwarf phenotype with shorter internodes</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B180">Sun X. et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc05g054360.3.1</td>
<td valign="top" align="center">6.837513657</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">Pectin methylesterase/<bold>flower initiation</bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B203">Wen et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">Solyc12g010500.2.1</td>
<td valign="top" align="center">5.358159809</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="left">U-box protein/<bold>biotic (resistance to <italic>X. perforans</italic></bold></td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref></td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn id="tfn1"><p><italic>The function was provided by SolGenomics Network annotation and by specific literature (in bold).</italic></p></fn>
</table-wrap-foot>
</table-wrap>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption><p>GOs distribution of differentially expressed genes (DEGs). Gene Ontology (GO) terms associated with upregulated (green bars) and downregulated (red bars) genes in the PhAN4 HRCs compared to control HRCs, based on &#x201C;Molecular Functions&#x201D; (MF), &#x201C;Biological Process&#x201D; (BP), &#x201C;Cellular Component&#x201D; (CC) and KEGG ontological domain.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g005.tif"/>
</fig>
<sec id="S3.SS3.SSS1">
<title>Gene Ontology Enrichment Analysis</title>
<p>Molecular function (MF) resulted in the most abundantly represented GO category, with 9 GO terms and an intersection size of 15 genes over a query size of 165 genes. The most enriched terms were related to &#x2018;enzyme inhibitory activity,&#x2019; with nine upregulated DEGs, seven of which are classified as serine-type endopeptidase inhibitors in tomatoes. Among them, Solyc03g020080.3.1, Solyc03g020030.3.1, Solyc11g020960.2.1, Solyc08g080630.3.1, Solyc10g086090.2.1, Solyc10g086100.2.1 encode specific Pin-II type proteinase inhibitors or protease inhibitors that have been already demonstrated to be players of the defense against wounding, pathogens, and pests and of response to abiotic stress, especially UV, drought, and heat stress in tomato (<xref ref-type="bibr" rid="B15">Bergey et al., 1996</xref>; <xref ref-type="bibr" rid="B32">Conconi et al., 1996</xref>; <xref ref-type="bibr" rid="B52">Fan et al., 2020</xref>). Within MF also &#x2018;beta-glucosidase&#x2019; and &#x2018;glucosidase activity&#x2019; terms were represented with four upregulated DEGs. Among them, Solyc01g059965.1.1 has been demonstrated to be implicated in the defense of tomato plants against pathogens (<xref ref-type="bibr" rid="B135">Murata et al., 2019</xref>), and its expression has been found to be modulated in tomatoes upon infection with <italic>Cladosporium fulvum</italic> and <italic>Phytophthora infestans</italic> (<xref ref-type="bibr" rid="B193">van Kan et al., 1992</xref>; <xref ref-type="bibr" rid="B51">Fan et al., 2021</xref>). Upregulation of Solyc06g073760.3.1 has been correlated to increased softening of transgenic tomato overexpressing a MADS-box transcription factor, affecting fruit development and ripening (<xref ref-type="bibr" rid="B82">Huang et al., 2017</xref>).</p>
<p>Within the BP category, coherently with secondary metabolites analysis, the &#x2018;flavonoid biosynthetic process&#x2019; term was found. In particular, GOE analysis highlighted the upregulation of four genes: Solyc05g053550.3.1, Solyc09g091510.3.1, Solyc02g083860.3.1, Solyc02g085020.3.1. Solyc09g091510.3.1, and Solyc05g053550.3.1 are tomato <italic>chalcone synthase</italic> (<italic>CHS</italic>) I and II, respectively, that are early pathway genes that determine the accumulation of the naringenin chalcone precursor of anthocyanins and other flavonoids (<xref ref-type="bibr" rid="B212">Zhang et al., 2019</xref>). Solyc02g083860.3.1 is tomato <italic>Flavonoid-3-hydroxylase</italic> (<italic>F3H</italic>) that leads to the accumulation of dihydromyricetin, dihydrokaempferol, and dihydroquercetin precursors of anthocyanins and of other flavonoids in tomatoes (<xref ref-type="bibr" rid="B9">Aoki et al., 2010</xref>; <xref ref-type="bibr" rid="B212">Zhang et al., 2019</xref>). Solyc02g085020.3.1 is tomato <italic>dihydroflavonol reductase</italic> (<italic>DFR</italic>) that leads to the accumulation of leucoanthocyanidins in tomatoes (<xref ref-type="bibr" rid="B20">Bongue-Bartelsman et al., 1994</xref>).</p>
<p>Within the CC GO category, &#x2018;Extracellular Region&#x2019; and &#x2018;Casparian Strip&#x2019; terms were categorized. Seventeen genes over a query size of 115, were found to be upregulated within these terms. These genes, in many cases, are specifically correlated to lignin biosynthesis, cell wall organization, and resistance to abiotic and biotic stress functions in tomatoes. In particular, Solyc05g052245.1.1 and Solyc09g010860.3.1 are the tomato expansins A8-like and EXPA4, involved in cell wall organization (<xref ref-type="bibr" rid="B33">Consortium et al., 2012</xref>). Solyc02g062510.3.1, which shares 86% homology with the <italic>S. tuberosum</italic> Peroxidase 72-like gene, and Solyc02g077300.2.1 (tomato Peroxidase 19) are involved in the phenylpropanoids biosynthesis (<xref ref-type="bibr" rid="B129">Mei et al., 2009</xref>). In addition, also Solyc04g080760.3.1 (tomato Peroxidase 9) plays a role in hypoxia tolerance and maintaining the iron balance in tomato (<xref ref-type="bibr" rid="B160">Safavi-Rizi et al., 2020</xref>). Peroxidase 9 was also demonstrated to be a pathogenesis-related protein upregulated upon <italic>Tomato Mosaic Virus</italic> infection (<xref ref-type="bibr" rid="B8">Andolfo et al., 2014</xref>). Solyc06g054320.1.1, Solyc10g055190.1.1, Solyc10g055200.1.1, and Solyc04g010270.1.1 represent tomato dirigent proteins that contribute to the dimerization of conyferil alcohol, a crucial step toward lignin biosynthesis, modulating cell wall metabolism during abiotic and biotic stress exposure in tomato (<xref ref-type="bibr" rid="B142">Paniagua et al., 2017</xref>). Solyc01g110110.3.1 and Solyc02g076710.3.1 are tomato cysteine proteinases. In particular, Solyc02g076710.3.1 shares 90% homology with <italic>N. benthamiana</italic> cathepsin B-like cysteine proteases that are involved in the hypersensitive response (<xref ref-type="bibr" rid="B127">McLellan et al., 2009</xref>). Solyc08g080630.3.1, already highlighted as an upregulated DEG within the MF category GOE, is the tomato <italic>SlPI31</italic> protease inhibitor. This gene has been demonstrated to be upregulated under <italic>Tomato Spotted Wilt Virus</italic> infection in tomato roots and leaves and has been shown to be upregulated in drought-tolerant tomato lines and drought-sensitive varieties under drought conditions (<xref ref-type="bibr" rid="B52">Fan et al., 2020</xref>).</p>
<p>Gene ontology enrichment (GOE) analysis revealed only one downregulated DEG (<xref ref-type="supplementary-material" rid="FS4">Supplementary File 4</xref>) belonging to the Molecular Function term &#x2018;glycosyl transferase.&#x2019; Solyc05g053890.2.1 represents the complete sequence of the tomato UDP-GT-like which is probably related to glycosylation of flavonoids prior to their transport to the vacuole (Solyc04g016200.1.1, Solyc04g016210.3.1, Solyc05g053890.2.1, Solyc01g095760.3.1 are incomplete sequences of tomato UDP-GT-like) (<xref ref-type="bibr" rid="B57">Fernandez-Moreno et al., 2016</xref>).</p>
</sec>
<sec id="S3.SS3.SSS2">
<title>Differentially Expressed Genes Analysis</title>
<p>Despite no GOE being found in the Response to stimulus category, a relatively high number of DEGs was found that could be associated with response to abiotic and biotic stress response. Fifteen upregulated and seven downregulated DEGs were found to be correlated with such response. Among upregulated DEGs involved in early signals of defense responses against environmental cues, Solyc01g096560.2.1 (Log<sub>2</sub>Fc = 4,10; <italic>TomLOXD</italic>; <xref ref-type="supplementary-material" rid="FS3">Supplementary File 3</xref>), was retrieved. <italic>TomLOXD</italic> encodes a lipoxygenase that has been demonstrated to elevate wound-induced jasmonate response, upregulation of wound-induced genes, and enhanced resistance to insects and necrotrophic pathogens in tomatoes (<xref ref-type="bibr" rid="B206">Yan et al., 2013</xref>). Solyc07g054840.3.1 (Log<sub>2</sub>Fc = 3.34; tomato transcription factor 41) shares the best homology with Myb41 of <italic>A. thaliana</italic> where it functions as a Map-kinase involved in several signaling pathways that control plant development and salt stress tolerance (<xref ref-type="bibr" rid="B79">Hoang et al., 2012</xref>). Solyc03g095810.3.1 (Log<sub>2</sub>Fc = 6.92; tomato Trichome birefringence-like protein) upregulation mediates xylan acetylation and has been demonstrated essential in tomatoes for invading microorganism resistance and against environmental stress like cold and drought (<xref ref-type="bibr" rid="B216">Zhang et al., 2020</xref>). Solyc10g007970.2.1 (Log<sub>2</sub>Fc = 6.96; tomato WRKY transcription factor 77) has been demonstrated to be involved in the signaling to water deficit in tomatoes (<xref ref-type="bibr" rid="B10">Asins et al., 2021</xref>). Solyc07g043690.2.1 (Log<sub>2</sub>Fc = 2.80; tomato <italic>SlNPR1</italic>) has been suggested to regulate tomato plant drought response (<xref ref-type="bibr" rid="B105">Li J. et al., 2019</xref>). Solyc03g096460.3.1 (Log<sub>2</sub>Fc = 2.3) is a known modulator of wound signaling in tomatoes (<xref ref-type="bibr" rid="B167">Scranton et al., 2013</xref>). Solyc02g080790.3.1 (Log<sub>2</sub>Fc = 3.31; tomato deoxypusine synthase <italic>SlDHS</italic>) has been shown to be upregulated during osmotic stress and chilling injury (<xref ref-type="bibr" rid="B202">Wang et al., 2001</xref>; <xref ref-type="bibr" rid="B72">Gupta et al., 2013</xref>). Solyc10g081300.1.1 (Log<sub>2</sub>Fc = 2.56; <italic>SlMC8</italic>), encodes a metacaspase that is upregulated during apoptosis induction by pests and regulated by drought, cold, and salt in tomatoes (<xref ref-type="bibr" rid="B112">Liu et al., 2016</xref>). Solyc10g080690.2.1 (Log<sub>2</sub>Fc = 2.3; tomato patatin defense protein) has been demonstrated to be upregulated upon soil flooding in tomatoes (<xref ref-type="bibr" rid="B39">de Ollas et al., 2021</xref>). Solyc06g073760.3.1 (Log<sub>2</sub>Fc = 4.07; tomato &#x03B2; 1,3-glucanase 2 <italic>BGL2</italic>) has been found to be negatively correlated with the sugar/organic acid ratio of tomato fruits (<xref ref-type="bibr" rid="B107">Li et al., 2021</xref>). The simultaneous upregulation of <italic>BGL2</italic> and <italic>PR1</italic>, the marker genes of the salicylic acid (SA) pathway, is a hallmark of systemic resistance induced in tomato plants against different pathogens and can be followed by accumulation of SA at high levels (<xref ref-type="bibr" rid="B145">Peng et al., 2004</xref>; <xref ref-type="bibr" rid="B50">Fahim et al., 2016</xref>; <xref ref-type="bibr" rid="B75">Hanan et al., 2020</xref>). Solyc12g035225.1.1 (Log<sub>2</sub>Fc = 9.26; tomato putative zinc-finger domain-containing protein) shares 75% homology with rice <italic>RICESLEEPER1</italic> that was found to be upregulated in <italic>S. chilense</italic> in relation to transcription factors for salt tolerance (<xref ref-type="bibr" rid="B90">Kashyap et al., 2020</xref>). Solyc12g010500.2.1 and Solyc12g010670.1.1 (Log<sub>2</sub>Fc = 5.35 and 5.36, respectively) are categorized as E3 ubiquitin proteins that have been found to be upregulated in tomato genotypes resistant to <italic>Xanthomonas perforans</italic> (<xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref>). Solyc12g009630.2.1 (Log<sub>2</sub>Fc = 5.18; tomato calmodulin <italic>SlCaM3</italic>), encodes an important calcium-binding protein that has been found to be upregulated in tomato stem and roots upon <italic>Botrytis cinerea</italic> infection and mechanical wounding (<xref ref-type="bibr" rid="B144">Peng et al., 2014</xref>). In addition, it has been reported that <italic>SlCaM3</italic> is strongly expressed under salt and cold stress in tomatoes (<xref ref-type="bibr" rid="B172">Shi and Du, 2020</xref>). Solyc02g067750.3.1 (Log<italic><sub>2</sub></italic>Fc = 6.91) shares 80% identity with <italic>N. benthamiana CA1</italic>. During drought stress CA1 proteins gradually diminish within the chloroplast and are accumulated in the cytosol, suggesting that they could be translocated from chloroplasts to the cytosol and act as a signal messenger from the chloroplast in tomato (<xref ref-type="bibr" rid="B109">Li P. et al., 2020</xref>). Importantly, in view of the possible improvement of resistance to abiotic stresses relevant to space, Solyc08g075705.1.1 (Log<sub>2</sub>Fc = 4.25; tomato plastidial thioredoxin Y2, <italic>pTRX y2</italic>) was found to be upregulated. PTRX y2 together with pTRX y1 and x-type TRXs is mostly involved in ROS detoxification and takes part in the complex redox signaling network regulating tomato plant development (<xref ref-type="bibr" rid="B169">Serrato et al., 2013</xref>).</p>
<p>Among downregulated DEGs correlated with resistance functions, Solyc09g007190.3.1 (Log<italic>2</italic>Fc = &#x2212;2.21; tomato peroxiredoxin-like 2A PRXL2A) redox regulatory protein was found. Solyc03g098760.2.1 (Log<sub>2</sub>Fc = &#x2212;5.1; tomato proteinase inhibitor I3 Kunitz-type trypsin inhibitor) has been demonstrated to be upregulated upon the cell-content feeding mite <italic>Tetranychus</italic> species infection (<xref ref-type="bibr" rid="B164">Schimmel et al., 2018</xref>) and it is told to protect seeds from predators (<xref ref-type="bibr" rid="B87">Islam et al., 2015</xref>). Solyc09g089490.3.1 (Log<sub>2</sub>Fc = &#x2212;5.21; tomato SlPI40 protease inhibitor) can be induced by abiotic (drought and salt) and biotic (<italic>Botrytis cinerea</italic> and <italic>Tomato Spotted Wilt Virus</italic>) stress (<xref ref-type="bibr" rid="B52">Fan et al., 2020</xref>). Solyc06g008760.1.1 (Log<sub>2</sub>Fc = &#x2212;3.05; tomato <italic>Glutaredoxin-C13-like</italic>) has been demonstrated to be upregulated in ripening inhibitor (<italic>rin</italic>) mutants of <italic>S. lycopersicum</italic> (<xref ref-type="bibr" rid="B100">Kumar et al., 2016</xref>). Solyc07g055610.2.1 (Log<sub>2</sub>Fc = &#x2212;2.05); tomato Resistance protein R1) has been related to resistance to late blight (<xref ref-type="bibr" rid="B21">Bournival et al., 1989</xref>) and it has been shown to be linked to proteinase inhibitor I3 upon <italic>Fusarium oxysporum</italic> infection (<xref ref-type="bibr" rid="B21">Bournival et al., 1989</xref>; <xref ref-type="bibr" rid="B140">Pan et al., 2000</xref>). Solyc01g010480 (Log<sub>2</sub>Fc = &#x2212;2.2; tomato K+ channel KAT1) was demonstrated to be highly upregulated in low K tolerant tomato genotypes upon potassium deficiency (<xref ref-type="bibr" rid="B217">Zhao et al., 2018</xref>). Solyc01g102610.3.1 (Log2Fc = &#x2212;3.60; tomato FRO6) is involved in nutrient transport in phloem and was observed to be downregulated under <italic>Phytoplasma solani</italic> infection of tomato (<xref ref-type="bibr" rid="B25">Buoso et al., 2019</xref>).</p>
<p>Despite GOE retrieving only four genes among the &#x2018;flavonoid biosynthetic process&#x2019; term, many other upregulated DEGs resulted in the analysis that is associated with biosynthesis of anthocyanins and other specialized metabolites (<xref ref-type="fig" rid="F6">Figure 6</xref>). Twelve additional structural genes and six transcription factors were identified as upregulated DEGs. In addition to <italic>CHS, F3H</italic> and <italic>DFR</italic>, DEGs analysis revealed also tomato naringenin-chalcone isomerase (<italic>CHI</italic>) (Solyc05g010320.3.1; Log<sub>2</sub>Fc = 4.30 and Solyc05g052240.3.1; Log<sub>2</sub>Fc = 8.45), tomato flavonoid-3&#x2032;,5&#x2032;-hydroxylase <italic>F3</italic>&#x2032;<italic>5</italic>&#x2032;<italic>H</italic> (Solyc11g066580.2.1; Log<sub>2</sub>Fc = 16.35), tomato anthocyanin synthase <italic>ANS</italic> (Solyc08g080040.3.1, Log<sub>2</sub>Fc = 8.86) were found. Interestingly, also Solyc04g078140.3.1, which shares the best homology with <italic>Cytochrome b5</italic> of <italic>P. hybrida</italic>, where it is essential for full activity of <italic>F3&#x2032;5&#x2032;H</italic>, was upregulated (Log<sub>2</sub>Fc = 8.35) (<xref ref-type="bibr" rid="B41">de Vetten et al., 1999</xref>). In addition, tomato caffeoyl-CoA-<italic>O</italic>-methyltransferase Solyc09g082660.3.1; Log<sub>2</sub>Fc = 15.0503), already identified as the prime candidate gene responsible for anthocyanin methylation in tomatoes due to significant correlation of expression with <italic>ANS, DFR</italic>, and <italic>F3&#x2032;5&#x2032;H</italic> in <italic>Rosea1</italic> and <italic>Delila</italic> fruits (<xref ref-type="bibr" rid="B156">Roldan et al., 2014</xref>), resulted upregulated. It shares the best homology with <italic>P. hybrida O</italic>-methyltransferase (<italic>OMT</italic>). Interestingly, it was found to have a significant correlation with abiotic stress in tomatoes (<xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref>). Three tomato UDP-glucose flavonoid 3-<italic>O</italic>-glucosyl transferases (<italic>3UFGT</italic>) (Solyc02g062975.1.1, Log<sub>2</sub>Fc = 7.08; Solyc10g083440.1.1, Log<sub>2</sub>Fc = 9.97; Solyc12g098590.2.1, Log<sub>2</sub>Fc = 16.55) catalyzing the transfer of the glucosyl moiety from UDP-glucose to the 3-hydroxyl group of anthocyanidins in tomato were found among upregulated DEGs, as well (<xref ref-type="bibr" rid="B81">Hu et al., 2011</xref>; <xref ref-type="bibr" rid="B188">Tohge et al., 2020</xref>). Furthermore, anthocyanidin-3-<italic>O</italic>-glucoside rhamnosyltransferase (<italic>3RT</italic>) (Solyc09g059170.2.1, Log<sub>2</sub>Fc = 8.3262), which in tomato controls the conversion of anthocyanidin-3-glucosides to anthocyanidin-3-rutinosides by the UDP rhamnose, was found among upregulated DEGs (<xref ref-type="bibr" rid="B188">Tohge et al., 2020</xref>). Tomato anthocyanin acyltransferase (<italic>AAT</italic>, or Flavonoid-3-<italic>O</italic>-rutinoside-4&#x201D;&#x2019;-<italic>O</italic>-phenylacyltransferase; Solyc12g088170.2.1, Log<sub>2</sub>Fc = 13.21) resulted upregulated, as well. Solyc02g081340.3.1 (Log<sub>2</sub>Fc = 10.53) resulted among upregulated DEGs. In tomato, it encodes a putative Glutathione S-Transferase that shares 84% homology with <italic>P. hybrida GST</italic> that is responsible for anthocyanin sequestration in the vacuole (<xref ref-type="bibr" rid="B4">Alfenito et al., 1998</xref>). Solyc03g025190.4.1 (Log<sub>2</sub>Fc = 16.80; tomato <italic>MTP77</italic>) resulted highly upregulated among DEGs. This gene belongs to clade 1 of the multidrug and toxic compound extrusion (MATE) family member (<italic>Transparent testa 2-like</italic>), which in tomato has been associated with vacuolar chloride channels related to the regulation of cell turgescence. In Micro-Tom, many MATE belonging to clade 1 have been functionally related to the transport of secondary metabolites (<xref ref-type="bibr" rid="B48">dos Santos et al., 2017</xref>). Solyc10g006120.2.1 (Log<sub>2</sub>Fc = 7) was found to be upregulated, as well. This gene shares 59% sequence identity with leucoanthocyanidin dioxygenase (<italic>LDOX</italic>) from <italic>P. hybrida</italic> and 61% with <italic>S. tuberosum FLS</italic> (<xref ref-type="bibr" rid="B143">Pelletier et al., 1997</xref>). LDOX has been demonstrated to be a bi-functional enzyme being able both to convert leucoanthocyanidins into anthocyanidins and to catalyze the <italic>in planta</italic> formation of flavonols in fls1-2 mutants of <italic>A. thaliana</italic> (<xref ref-type="bibr" rid="B150">Preu&#x00DF; et al., 2009</xref>).</p>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption><p>Schematic diagram of the anthocyanin biosynthetic pathway. The structural genes upregulated by ectopic expression of <italic>PhAN4</italic> in MicroTom HRCs and leading to accumulation of compounds are in black and marked by red boxes. PAL, phenylalanine ammonia-lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumarate CoA ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3&#x2032;H, flavonoid-3&#x2032;-hydroxylase; F3&#x2032;5&#x2032;H, flavonoid-3&#x2032;,5&#x2032;-hydroxylase; DFR, dihydroflavonol reductase; ANS, anthocyanin synthase; OMT, O-methyltransferase; AAT, anthocyanin acyltransferase; RT, rhamnosyltransferase; UFGT, UDP-glucose flavonoid 3-<italic>O</italic>-glucosyl transferase; AA7GT, cyanidin-3-<italic>O</italic>-glucoside-7-<italic>O</italic>-glucosyltransferase; ANP, anthocyanin permease; GST, glutathione-<italic>S</italic>-transferase.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g006.tif"/>
</fig>
<p>Together with the regulation of structural genes, <italic>PhAN4</italic> positively modulated also transcription factors involved in anthocyanin biosynthesis. Solyc07g052490.3.1 (Log<sub>2</sub>Fc = 7.17, tomato Myb-like transcription factor <italic>Atv</italic>) is involved in anthocyanin biosynthesis (<xref ref-type="bibr" rid="B28">Cao et al., 2017</xref>). Also, Solyc10g086290.2.1 (Log<sub>2</sub>Fc = 8.65), which shares 83% homology with <italic>Solanum tuberosum AN2-like</italic>, is a R2R3Myb involved in anthocyanin biosynthesis, was found (<xref ref-type="bibr" rid="B179">Sun C. et al., 2019</xref>; <xref ref-type="bibr" rid="B31">Colanero et al., 2020</xref>; <xref ref-type="bibr" rid="B207">Yan et al., 2020</xref>). Solyc09g065100.2.1 (Log<sub>2</sub>Fc = 14.18) maps the Hoffman&#x2019;s anthocyaninless (AH) locus and encodes a bHLH factor (SlAN1) that positively regulates anthocyanin biosynthesis in tomatoes (<xref ref-type="bibr" rid="B152">Qiu et al., 2016</xref>). No effects of <italic>PhAN4</italic> expression were found on another known regulator of anthocyanins biosynthesis, <italic>AN11</italic>. Additionally, Solyc10g084380.1.1 was upregulated (Log<sub>2</sub>Fc = 3.43). In <italic>Solanum lycopersicum</italic>, this gene encodes a WRKY that shares 76% homology with <italic>PH3</italic> from <italic>Petunia hybrida</italic> where it regulates vacuolar acidification and boosts anthocyanin biosynthesis, as well (<xref ref-type="bibr" rid="B198">Verweij et al., 2016</xref>).</p>
<p>Among upregulated DEGs, putative repressors of anthocyanins biosynthesis were found. The upregulated Solyc12g005800.2.1 (Log<sub>2</sub>Fc = 7.51) is the tomato SlMYBATV-like (<xref ref-type="bibr" rid="B28">Cao et al., 2017</xref>), a R3-MYB repressor. Solyc10g083900.2.1 (Log<sub>2</sub>Fc = 3.54; tomato R2R3Myb transcription factor 27) shares the best homology with <italic>Myb27</italic> from <italic>P. hybrida</italic>, where it is a repressor of the synthesis of anthocyanins (<xref ref-type="bibr" rid="B2">Albert et al., 2011</xref>, <xref ref-type="bibr" rid="B1">2014</xref>) and Solyc01g095640.2.1 (Log<sub>2</sub>Fc = 4.92; tomato <italic>ETC3</italic> or <italic>SlTRY</italic>) orthologous in <italic>A. thaliana</italic> acts a repressor of anthocyanins accumulation, as well (<xref ref-type="bibr" rid="B189">Tominaga-Wada et al., 2013</xref>).</p>
<p>To complete the description related to the modulation of genes related to specialized metabolites, three DEGs resulted to be upregulated and three downregulated. Among upregulated DEGS, Solyc01g105880.4.1 and Solyc09g092470.2.1 (Log<sub>2</sub>Fc = 3.46 and 5.69, respectively; tomato monoterpenoid synthases 2 <italic>TPS4</italic> and <italic>TPS14</italic>), are involved in the biosynthesis of monoterpenes and sesquiterpenes, respectively. <italic>TPS4</italic> has been found to be upregulated in tomato cultivars resistant to <italic>Fusarium oxysporum</italic> (<xref ref-type="bibr" rid="B196">Vel&#x00E1;zquez-M&#x00E1;rquez et al., 2021</xref>). Solyc11g017240.2.1 (Log<sub>2</sub>Fc = 3.78; tomato chorismate mutase 2 <italic>SlCM2</italic>), catalyzes the first step of the shikimate pathway from phenylalanine to the volatile compounds responsible for tomato fruit aroma and quality and defense from biotic and abiotic stress response (<xref ref-type="bibr" rid="B191">Tzin et al., 2015</xref>). In tomatoes, <italic>SlCM2</italic> has been also shown to be upregulated under drought stress (<xref ref-type="bibr" rid="B59">Filiz et al., 2019</xref>). Among downregulated genes, Solyc08g008630.3.1 (Log<sub>2</sub>Fc = &#x2212;3.34; tomato chloroplastic beta-carotene isomerase D27 <italic>Dwarf27</italic>) is involved in strigolactone and beta-carotene biosynthesis and has been found to be downregulated in psyllid-infested tomato plants (<xref ref-type="bibr" rid="B76">Harrison et al., 2021</xref>). Solyc04g050930.3.1 (Log<sub>2</sub>Fc = &#x2212;2.07; tomato violaxanthin de-epoxidase <italic>VDE</italic>) is involved in the carotenoid biosynthesis. Suppression of <italic>VDE</italic> can induce the photo-inhibition of the PSII and, at the same time, it results in an accumulation of fucoxanthin that functions as an efficient anti-oxidant in anoxia conditions (<xref ref-type="bibr" rid="B188">Tohge et al., 2020</xref>). Moreover, it has been shown that <italic>VDE</italic> is downregulated in tomato plants upon <italic>Pseudomonas syringae</italic> pv. tomato DC3000 infection (<xref ref-type="bibr" rid="B209">Yang Y. X. et al., 2015</xref>). Solyc05g010180.3.1 (Log<sub>2</sub>Fc = &#x2212;2.22; tomato carotenoid isomerase <italic>CRTISO</italic>) is involved in carotenoids biosynthesis. In MicroTom fruits, the downregulation of carotenoid isomerase has been demonstrated to induce an accumulation of zeta-carotene and <italic>cis</italic>-prolycopene (<xref ref-type="bibr" rid="B48">dos Santos et al., 2017</xref>; <xref ref-type="bibr" rid="B60">Florio et al., 2021</xref>), both elevating and modifying carotenoid profiles toward more bioavailable forms compared to wild-type (<xref ref-type="bibr" rid="B143">Pelletier et al., 1997</xref>).</p>
<p>To complete the description related to DEGs that were modulated upon expression of <italic>PhAN4</italic> and that are related to plant physiology, in addition to Solyc06g073760.3.1 (already described in GOE analysis in the MF category), Solyc12g006140.2.1 (Log<sub>2</sub>Fc = 4.36; tomato chloroplastic light-harvesting chlorophyll a/b-binding protein 37) was found to be upregulated. Its upregulation was demonstrated to improve photosynthesis and in extending the shelf life in tomato plants (<xref ref-type="bibr" rid="B219">Zouari et al., 2014</xref>). Among downregulated DEGs, Solyc02g065220.3.1 (Log<sub>2</sub>Fc = &#x2212;2.14; tomato cytochrome P450) was shown to have significantly different transcript levels between purple and red sectors of VIGs <italic>Del/Ros</italic> tomatoes late ripening. Its downregulation has been associated with extended shelf life (<xref ref-type="bibr" rid="B64">Gao et al., 2018</xref>). Solyc09g066150.1.1 (Log<sub>2</sub>Fc = &#x2212;4.57; putative tomato cytochrome P450) suppression has been found in transgenic tomato plants unable to perform DNA methylation and its upregulation has been associated with fruit ripening (<xref ref-type="bibr" rid="B217">Zhao et al., 2018</xref>).</p>
</sec>
</sec>
<sec id="S3.SS4">
<title>Phenolic Content and Antioxidant (2,2-Diphenyl-1-Picrylhydrazyl) Activity</title>
<p>To verify whether <italic>PhAN4</italic> expression was associated with increased antioxidant activity, <italic>in vitro</italic> scavenging activity of the hydroalcoholic soluble fraction of HRCs was assessed by non-enzymatic 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay (<xref ref-type="bibr" rid="B40">de Torre et al., 2019</xref>). The total phenolic content (expressed as &#x03BC;g of gallic acid equivalents (GAE)/g of dry weight, DW) was found to be ninefold and eightfold compared to control (18.2 &#x00D7; 103 &#x03BC;g GAE/g DW in AN4-1 and 16.4 &#x00D7; 103 &#x03BC;g GAE/g DW AN4-GFP-8 HRCs (<xref ref-type="fig" rid="F7">Figure 7A</xref>). The trolox equivalent antioxidant capacity of the hydroalcoholic soluble fraction (containing anthocyanins) in purple HRCs appears to be thirty (in the AN4-1 clone) and twenty (in the AN4-GFP-8 clone) times higher than in control HRCs (<xref ref-type="fig" rid="F7">Figure 7B</xref>).</p>
<fig id="F7" position="float">
<label>FIGURE 7</label>
<caption><p>Total phenolic content in MicroTom transgenic HRCs reported in mg of gallic acid equivalents/g of dry weight <bold>(A)</bold>. Analysis of antioxidant activity (DPPH) in MicroTom transgenic HRCs reported as &#x03BC;g Trolox equivalents/g dry weight (DW) <bold>(B)</bold>. Each analysis consisted of triplicate measurements of each sample and data were averaged over the three measurements. A univariate statistical analysis based on Student&#x2019;s <italic>t</italic>-test and one way-ANOVA (<italic>P</italic> &#x2264; 0.05) was carried out.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g007.tif"/>
</fig>
</sec>
<sec id="S3.SS5">
<title>Electron Spin Resonance Analysis</title>
<p>To further characterize the effect of the ectopic expression of <italic>PhAN4</italic>, MicroTom HRC lyophilized material was investigated for its ability to counteract the generation of reactive oxygen species (ROS) and for the maintenance of this feature after high dose gamma radiation. The AN4-1 HRC was chosen as the best candidate to evaluate resistance to radiation by Electron Spin Resonance (ESR). This analysis assessed the amount of peroxyl radicals in lyophilized HRCs. The HRCs ESR signal is characterized by a singlet signal at 3454 Gauss, correspondent to peroxyl radicals induced by gamma irradiation (<xref ref-type="bibr" rid="B7">Andersen et al., 2000</xref>; <xref ref-type="bibr" rid="B83">Ichikawa et al., 2001</xref>; <xref ref-type="bibr" rid="B136">Nagata et al., 2003</xref>; <xref ref-type="bibr" rid="B158">Rossetto et al., 2007</xref>; <xref ref-type="bibr" rid="B49">Esatbeyoglu et al., 2014</xref>; <xref ref-type="bibr" rid="B55">Faure et al., 2014</xref>). Negligible satellite peaks below 3,440 and above 3,480 Gauss are present as well and are related to several different contributions (such as cellulose-like molecules and anthocyanins) (<xref ref-type="bibr" rid="B7">Andersen et al., 2000</xref>; <xref ref-type="bibr" rid="B190">Tuner and Korkmaz, 2007</xref>; <xref ref-type="bibr" rid="B146">Petrisor et al., 2008</xref>; <xref ref-type="bibr" rid="B49">Esatbeyoglu et al., 2014</xref>; <xref ref-type="bibr" rid="B55">Faure et al., 2014</xref>). Typical ESR spectra of HRCs irradiated at 2,000 Gy absorbed dose, are shown in <xref ref-type="fig" rid="F8">Figure 8A</xref>.</p>
<fig id="F8" position="float">
<label>FIGURE 8</label>
<caption><p>ESR spectra of AN4-1 and control HRCs gamma-irradiated at 2 kGy absorbed dose (dose rate = 1.8) <bold>(A)</bold>. ESR kGy water/h signal intensity of white and purple HRCs gamma are reported as a function of the absorbed dose (up to 2 kGy absorbed dose; dose rate = 1.8 kGy water/h) <bold>(B)</bold>. The intensity of each signal is expressed as the peak-to-peak height normalized for mass units and by subtracting the intensities of the HRCs signals before irradiation.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g008.tif"/>
</fig>
<p>The AN4-1 and control spectra before gamma radiation exposure do not show significant peaks (data not shown). After irradiation (0.5, 1, and 2 kGy), the control shows a signal intensity significantly higher than AN4-1 (<xref ref-type="fig" rid="F8">Figures 8A,B</xref>). In particular, AN4-1 shows only a negligible signal increase after irradiation from the lowest to the highest absorbed dose. On the contrary, control HRC shows a constant and nearly linear increase of singlet intensity, already evident at low absorbed doses.</p>
</sec>
<sec id="S3.SS6">
<title>Ultraviolet-Visible Absorbance Spectra</title>
<p>We have used UV-VIS analysis of HRC extracts to characterize the resistance to gamma irradiation of the phenolic compounds accumulated in the AN4-1 line. Before irradiation, both control and AN4-1 acidic extracts revealed the main peak at 280 nm, followed by another peak at 315&#x2013;320 nm (<xref ref-type="fig" rid="F9">Figure 9</xref>).</p>
<fig id="F9" position="float">
<label>FIGURE 9</label>
<caption><p>UV-VIS spectra of MicroTom HRCs before and after 2 kGy absorbed dose. In control, peaks at 280 nm and 320 nm indicate the presence of flavonols, hydroxycinnamic acids, tannins, and flavanols <bold>(A)</bold>. In AN4-1, the additional peak at 345 nm completes the flavonols group profile compared to control, while the peak at 525 nm represents anthocyanins. The curve in the region between 400 and 450 nm refers to possible glycosylation, precipitation, complexation of anthocyanins <bold>(B)</bold>.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g009.tif"/>
</fig>
<p>In accordance with metabolomic data, in the spectra obtained in absence of irradiation, peaks around 280 nm and 320 nm indicate the presence of flavonols, hydroxycinnamic acids, tannins, and flavanols (<xref ref-type="bibr" rid="B174">Sol&#x00EC;s-Oviedo and de La Cruz Pech-Canul, 2019</xref>). The shoulder at 345 nm together with that at 280 nm further defines the UV-VIS spectra of the flavonols in AN4-1 (<xref ref-type="bibr" rid="B161">Saha et al., 2021</xref>). Anthocyanins and anthocyanins associated with phenolic acids also produce peaks around 280 nm and 320 nm, respectively (<xref ref-type="bibr" rid="B174">Sol&#x00EC;s-Oviedo and de La Cruz Pech-Canul, 2019</xref>), contributing to the profile of AN4-1 HRCs in <xref ref-type="fig" rid="F7">Figure 7B</xref>. Anthocyanins result in an additional characteristic peak at 525 nm (<xref ref-type="bibr" rid="B200">Vivar-Quintana et al., 2002</xref>; <xref ref-type="bibr" rid="B36">da Silva et al., 2007</xref>; <xref ref-type="bibr" rid="B56">Fedenko et al., 2017</xref>), which, as expected, is observed in AN4-1 and not in control HRCs. Gamma irradiation determined a slight absorbance increase at 280 nm and a significant decrease at 320 nm in controls. On the contrary, these peaks remained unchanged in AN4-1. In AN4-1, the absorbance at 400&#x2013;450 nm is possibly an indication of glycosylation, precipitation, complexation with tannins of anthocyanins upon irradiation (<xref ref-type="bibr" rid="B161">Saha et al., 2021</xref>). Gamma irradiation determined a slight decrease of the absorbance at 525 nm in AN4-1, as confirmed by a slight discoloration of the root material after irradiation.</p>
</sec>
<sec id="S3.SS7">
<title>Photoluminescence Analysis</title>
<p>Photoluminescence emission spectra were analyzed to determine the resistance to misfolding and oxidation of MicroTom HRCs soluble proteins after gamma irradiation. Photoluminescence spectra of extracts containing soluble proteins from control (<xref ref-type="fig" rid="F10">Figure 10A</xref>) and AN4-1 HRCs (<xref ref-type="fig" rid="F10">Figure 10B</xref>) were produced. The mass-normalized emission spectra of not irradiated soluble protein samples are similar in controls and AN4-1 and are characterized by high peaks mainly corresponding to tryptophan (370 nm) (<xref ref-type="bibr" rid="B208">Yang H. et al., 2015</xref>; <xref ref-type="bibr" rid="B78">Hilaire et al., 2017</xref>) and its metabolic products such as kynurenine (470 nm) and 3-hydroxykynurenine (439 nm) (<xref ref-type="bibr" rid="B117">Lohmann et al., 1988</xref>; <xref ref-type="bibr" rid="B38">Daly et al., 2009</xref>; <xref ref-type="bibr" rid="B62">Gakamsky et al., 2017</xref>). In addition, a peak at 470 nm is indicative of the presence of carbamate anions (<xref ref-type="bibr" rid="B141">Pan et al., 2013</xref>). In control HRC, the 2 kGy absorbed dose caused a decrease of fluorescence emission intensity for all three peaks. In particular, the &#x0394;% photoluminescence intensity after and before the irradiation shows that the peak at 370 nm is reduced by 67.87%, the peaks at 439 nm and 470 nm by 37.5%, and 28.57%, respectively (<xref ref-type="fig" rid="F8">Figure 8A</xref>). In AN4-1 only the 370 nm peak decreased (&#x2212;27.64%), while a slight increase (+18.57%) of the kynurenine peak (470 nm) was present. No significant modifications were observed at 439 nm (<xref ref-type="fig" rid="F10">Figure 10B</xref>).</p>
<fig id="F10" position="float">
<label>FIGURE 10</label>
<caption><p>Photoluminescence spectra of control <bold>(A)</bold> and AN4-1 <bold>(B)</bold> HRCs and related mass-normalized emission intensities (tables) before and after 2 kGy gamma irradiation. Main peaks refer to tryptophan (370 nm), its degradation products kynurenine and 3-hydroxykynurenine (439 and 470 nm), and carbamate anion (470 nm).</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-830931-g010.tif"/>
</fig>
</sec>
</sec>
<sec sec-type="discussion" id="S4">
<title>Discussion</title>
<p>Anthocyanins are well known for their antioxidant and health-protection properties. Tomato has been already subjected to genetic manipulation for improved levels and composition of these high-value compounds (<xref ref-type="bibr" rid="B163">Schauer et al., 2006</xref>; <xref ref-type="bibr" rid="B96">Klee and Tieman, 2013</xref>; <xref ref-type="bibr" rid="B67">Giovannoni, 2018</xref>; <xref ref-type="bibr" rid="B201">Wang et al., 2019</xref>). Nutraceutical improvement of tomato is expected to provide a nourishing food source for future long-term manned space missions such as NASA&#x2019;s &#x201C;Artemis&#x201D; lunar exploration program. The Artemis initiative includes sending a suite of new technology demonstrators to establish a sustained human presence by 2028 (<xref ref-type="bibr" rid="B45">DeZwart and Henderson, 2021</xref>). Low-power systems to grow plants will have the role to provide fresh and nutritious food to supplement astronauts&#x2019; diet and provide psychological benefits. The experiments conducted in the VEGGIE module onboard the International Space Station over the last few years have pioneered this scenario (<xref ref-type="bibr" rid="B205">Wolff et al., 2014</xref>; <xref ref-type="bibr" rid="B61">Fu et al., 2016</xref>; <xref ref-type="bibr" rid="B124">Massa et al., 2016</xref>; <xref ref-type="bibr" rid="B210">Zabel et al., 2016</xref>; <xref ref-type="bibr" rid="B84">Imhof et al., 2018</xref>).</p>
<p>The space environment, totally unusual for plants, can affect their metabolic processes and, consequently, growth, due to high-energy ionizing radiation, microgravity, magnetic field, and ultra-vacuum (<xref ref-type="bibr" rid="B204">Williams et al., 2004</xref>; <xref ref-type="bibr" rid="B118">Lotito and Frei, 2006</xref>; <xref ref-type="bibr" rid="B132">Moghaddam et al., 2011</xref>; <xref ref-type="bibr" rid="B184">Thamaphat et al., 2015</xref>; <xref ref-type="bibr" rid="B192">van Hoeck et al., 2017</xref>). Among abiotic stresses that plants will have to cope with in extraterrestrial environments artificially adapted to space agriculture, pro-oxidant stimuli are, indeed, the most prominent, due to cosmic ionizing radiation. Acting directly and indirectly to delay oxidative damage, enzymatic players, and metabolites activating endogenous antioxidant defense systems may help plant growth in the space environment. ROS attack plant cells causing loss of their structure and function (<xref ref-type="bibr" rid="B194">Vandenhove et al., 2010</xref>; <xref ref-type="bibr" rid="B132">Moghaddam et al., 2011</xref>; <xref ref-type="bibr" rid="B120">Marcu et al., 2013a</xref>; <xref ref-type="bibr" rid="B195">Vardhan and Shukla, 2017</xref>; <xref ref-type="bibr" rid="B71">Gudkov et al., 2019</xref>), rapidly reacting with almost all structural and functional organic molecules in the plant cells and causing irreversible oxidative damage on DNA, lipids, and proteins (<xref ref-type="bibr" rid="B162">Scandalios, 2002</xref>; <xref ref-type="bibr" rid="B170">Sewelam et al., 2016</xref>). The issue of counteracting overproduction of free radicals generated by harmful ionizing radiation is crucial for human survival in space outposts, as well, and opens the way to the ideal &#x2018;anti-oxidant space fresh food.&#x2019; Indeed, the oral intake of clinically tested chemical radioprotectants (i.e., thiols, aminothiols, thiadiazoles, and benzothiazoles) is limited due to toxicity (<xref ref-type="bibr" rid="B35">Copp et al., 2013</xref>). Therefore, there is great interest in the development of natural antioxidants possibly produced by plants and introduced with the diet (<xref ref-type="bibr" rid="B68">G&#x00F3;mez et al., 2021</xref>). Together with the above-mentioned abiotic &#x2018;macro-stresses,&#x2019; plants intended for space agriculture will have to cope with a plethora of abiotic &#x2018;micro-stresses&#x2019; related to the different cultivation environment/systems that will be adopted. Furthermore, plants will have to share with humans future crewed space habitats (spaceflights, planetary outposts, and life-support systems) where stringent microbial quality requirements may not be achieved (<xref ref-type="bibr" rid="B5">Amalfitano et al., 2020</xref>).</p>
<p>Plants have an intrinsic potential for adaptation as the heritage of ancestors that survived in the harsh initial terrestrial environments (<xref ref-type="bibr" rid="B42">de Vries and Archibald, 2018</xref>). The &#x2018;design&#x2019; of plant ideotypes suitable to these environments may be achieved by further refinement of existing biochemical and physiological features, such as specialized metabolites, that plants use to survive stress. Novel genotypes boosting biosynthetic pathways for the production of specialized metabolites can be generated by manipulation of their regulators. Among regulators, there are MYB transcription factors, known for their contribution to the increased complexity of land plants and to be regulators of plant responses to the environment (<xref ref-type="bibr" rid="B116">Lloyd et al., 2017</xref>; <xref ref-type="bibr" rid="B64">Gao et al., 2018</xref>; <xref ref-type="bibr" rid="B90">Kashyap et al., 2020</xref>; <xref ref-type="bibr" rid="B173">Shi and Panthee, 2020</xref>). Members of this large family of regulators are key players in the modulation, among others, of the biosynthesis of flavonoids, like anthocyanins, in different plant parts and response to all kinds of stimuli (<xref ref-type="bibr" rid="B6">Ambawat et al., 2013</xref>; <xref ref-type="bibr" rid="B113">Liu et al., 2015</xref>; <xref ref-type="bibr" rid="B159">Roy, 2016</xref>). MicroTom is extremely compact, early yielding, and would be suitable for agriculture in the confined area of a crewed space module. Here, we described the ectopic expression of the anthocyanin R2R3-MYB regulator <italic>PhAN4</italic> from <italic>Petunia hybrida</italic> in MicroTom hairy roots as a testbed for future engineered whole plants. As known, anthocyanin production is regulated by R2R3-MYB, bHLH, WDR, and WRKY cooperation (MBWW transcriptional complex) (<xref ref-type="bibr" rid="B175">Spelt et al., 2000</xref>; <xref ref-type="bibr" rid="B97">Koes et al., 2005</xref>). In this complex, the R2R3-MYB transcription factor is probably the limiting factor, in that the WDR and bHLH proteins are thought to be constitutively expressed (<xref ref-type="bibr" rid="B214">Zhang et al., 2013</xref>, <xref ref-type="bibr" rid="B215">2014</xref>). When specific MYB proteins are expressed in plants, this induces anthocyanin accumulation. Since some specific MYB transcription factors can function in regulating not only the biosynthesis of anthocyanins but also other traits (<xref ref-type="bibr" rid="B122">Meng et al., 2015</xref>; <xref ref-type="bibr" rid="B195">Vardhan and Shukla, 2017</xref>; <xref ref-type="bibr" rid="B88">Jian et al., 2019</xref>), we investigated if <italic>PhAN4</italic> may affect, together with accumulation of anthocyanins, features associated with improved traits related to survival in harsh and confined environments such as future space outposts.</p>
<p>Differently from the wealth of literature available on whole transgenic plants and cell culture systems, data concerning anthocyanins production are limited for hairy roots. To date, no data are available on anthocyanin accumulation in tomato hairy roots by metabolic engineering to make comparisons with our work. Although not comparable to levels achieved in transgenic plants (<xref ref-type="bibr" rid="B26">Butelli et al., 2008</xref>; <xref ref-type="bibr" rid="B149">Povero et al., 2011</xref>; <xref ref-type="bibr" rid="B93">Kiferle et al., 2015</xref>), accumulation of anthocyanins occurred in MicroTom HRCs upon <italic>PhAN4</italic> transformation, as expected due to the nature of the transgene. Importantly, no significant variation of transformed HRCs growth rates was found compared to controls. This gives a clue about the non-detrimental activity of <italic>PhAN4</italic> toward primary metabolism in this system.</p>
<p>In accordance with literature related to transgenic tomato plants (<xref ref-type="bibr" rid="B26">Butelli et al., 2008</xref>; <xref ref-type="bibr" rid="B177">Su et al., 2016</xref>; <xref ref-type="bibr" rid="B88">Jian et al., 2019</xref>), mass spectrometry allowed us to identify glycosylated and acylated delphinidin and petunidin as the most abundant anthocyanins in <italic>PhAN4</italic> HRCs. Interestingly, two additional anthocyanins, unusual in tomato, pelargonidin-3-glucoside, and malvidin-3-<italic>O</italic>-(4&#x201D;&#x2019;coumaroyl)-rutinose-5-<italic>O</italic>-glucose, were detected, as well. Malvidin and Pelargonidin derivatives have already been detected in <italic>Del</italic> and <italic>Ros1</italic> and <italic>LC</italic> and <italic>C1</italic> tomato plants, respectively (<xref ref-type="bibr" rid="B22">Bovy et al., 2002</xref>; <xref ref-type="bibr" rid="B177">Su et al., 2016</xref>). Interestingly, pelargonidin plays a major role in reducing genotoxic stress induced by environmental toxicants in plants (<xref ref-type="bibr" rid="B91">Khandelwal and Abraham, 2014</xref>). In addition, rather than other anthocyanins, pelargonidin-3-glucoside, that was accumulated in engineered MicroTom HRCs, has high bioavailability, being absorbed in an intact form into the gastrointestinal wall, undergoing first-pass metabolism and entering the systemic circulation as 4-hydroxybenzoic acid, a stable metabolite that is considered one of the main players of the systemic health effects of anthocyanins (<xref ref-type="bibr" rid="B53">Fang, 2014</xref>). In order to achieve a better understanding of <italic>PhAN4</italic> in the tomato hairy root phenylpropanoid pathway, we measured 14 phenolic acids and derivatives and 29 flavonoids: notably, a reduction in the content of some members of the former, and a massive increase in most of the compounds in the latter were observed, thus proving <italic>PhAN4</italic> is able to trigger the metabolic flux at both flavonoid and anthocyanin levels.</p>
<p>Data on the accumulation of anthocyanins and phenylpropanoids obtained by mass spectrometry was supported by transcriptome-wide RNA-seq analysis. RNA-seq, in complex, depicted a reprogramming oriented not only to anthocyanin accumulation, as expected, but also to positive regulation of cell response to biotic and abiotic stress and, possibly, to fruit quality-related traits.</p>
<p>Expression of <italic>PhAN4</italic> increased the transcript levels of almost all of the genes encoding enzymes required for anthocyanin biosynthesis with the exception of <italic>PAL, C4H, 4CL, F3&#x2032;H</italic>, and <italic>5UFGT</italic>. To facilitate comparisons, transcriptomic research on tomato plants for anthocyanins enrichment has been summarized in <xref ref-type="table" rid="T2">Table 2</xref>. <italic>CHS</italic> and <italic>CHI</italic> had been already found to be upregulated by overexpression of <italic>SlAN2</italic> in tomatoes, but not by ectopic expression of <italic>Del/Ros</italic> that, in turn, were able to upregulate <italic>F3H</italic> (<xref ref-type="bibr" rid="B26">Butelli et al., 2008</xref>; <xref ref-type="bibr" rid="B88">Jian et al., 2019</xref>). <italic>DFR</italic> had been already shown to be upregulated in the stem and leaf of tomato plants overexpressing <italic>SlAN2</italic> and <italic>SlAN1</italic> R2R3-MYBs (<xref ref-type="bibr" rid="B93">Kiferle et al., 2015</xref>). Interestingly, despite <italic>FLS</italic> was not found among upregulated DEGs in <italic>PhAN4</italic> HRCs, <italic>LDOX</italic>, a known bi-functional enzyme being able not only the conversion of leucoanthocyanidins in anthocyanidins but also to catalyze the formation of flavonols, resulted to be differentially upregulated in <italic>PhAN4</italic> HRCs. This may explain the accumulation of quercetin, kaempferol derivatives, and myricetin together with anthocyanidins. The flavonol biosynthetic activity of the upregulated <italic>LDOX</italic> is counterbalanced by the upregulated <italic>DFR</italic>. In tomatoes, DFR has a substantial preference for dihydromyricetin, which can be also derived by dihydrokaempferol and dihydroquercetin by F3&#x2032;5&#x2032;H activity. Interestingly, <italic>DilFl</italic> a tomato homolog of cytochrome b5 of <italic>P. hybrida</italic>, where it is essential for full activity of F3&#x2032;5&#x2032;H, was found to be upregulated in <italic>PhAN4</italic> HRCs. These findings may explain the differential accumulation of delphinidin and petunidin compared to pelargonidin, malvidin, and cyanidin (the latter was not detected at all). Among late biosynthetic genes, upregulation of <italic>ANS</italic> had been already shown upon <italic>SlAN2</italic> over-expression and <italic>Del/Ros</italic> expression in tomatoes. <italic>OMT</italic> and <italic>AAT</italic> transferases have already been described to be targets of a MYB in tomatoes, as well (<xref ref-type="bibr" rid="B212">Zhang et al., 2019</xref>). Their upregulation in <italic>PhAN4</italic> HRCs, together with that of <italic>GST, PH3, OMT, 3UFGT, RT</italic>, and <italic>AAT</italic> may explain the accumulation of the glycosylated and acylated forms of anthocyanidins. In particular, the function of the upregulated <italic>PH3</italic> (Solyc10g084380.1.1) in <italic>PhAN4</italic> HRC is rather to be associated with anthocyanin biosynthesis boosting than with acidification of pH, as tomato lacks <italic>PH1</italic> and <italic>PH5</italic> (i.e., the genes encoding the vacuolar P-ATPases which cooperate with PH3 and PH4 in determining flower color by hyperacidification of petal cell vacuoles in <italic>Petunia</italic>). Nevertheless, preliminary evaluation of pH of <italic>PhAN4</italic> and control HRC homogenates (<xref ref-type="bibr" rid="B197">Verweij et al., 2008</xref>) does not allow to exclude that the acidification function may occur (<xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 5</xref>), given that pH differences between <italic>PhAN4</italic> and control HRC seem to be in accordance with variations recorded between vacuolar P-ATPases-defective mutants and wild type <italic>Petunia hybrida</italic> (<xref ref-type="bibr" rid="B54">Faraco et al., 2014</xref>). The upregulation of anthocyanin biosynthesis-relevant transcription factors further expands the influence of <italic>PhAN4</italic> MYB in tomato gene expression regulation. Among those, the upregulation of <italic>SlAN1</italic>, <italic>SlAN2</italic>, and <italic>WD40</italic> are coherent with already proposed models of anthocyanin biosynthesis regulation (<xref ref-type="bibr" rid="B97">Koes et al., 2005</xref>; <xref ref-type="bibr" rid="B114">Liu et al., 2018</xref>).</p>
<table-wrap position="float" id="T2">
<label>TABLE 2</label>
<caption><p>Summary of results from the main research on tomato plants enrichment with anthocyanins obtained by both conventional breeding and genetic engineering approaches.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Tomato line</td>
<td valign="top" align="left">Origin</td>
<td valign="top" align="left">Main overexpressed genes</td>
<td valign="top" align="left">Main anthocyanins detected</td>
<td valign="top" align="left">Anthocyanin concentration</td>
<td valign="top" align="left">References</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">V118</td>
<td valign="top" align="left">Breeding</td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left">Pet-3-(p-coumaryl)-rut-5-glc;<break/> Pet-3-caeoyl-rut-5-glc;<break/> Mal-3(p-coumaryl)-rut-5-glc</td>
<td valign="top" align="left">50.18 mg 100 g<sup>&#x2013;1</sup> DW<break/> 9.04 mg 100 g<sup>&#x2013;1</sup> DW<break/> 13.09 mg 100 g<sup>&#x2013;1</sup> DW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B104">Li et al., 2011</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>Aft/Aft</italic> &#x00D7; <italic>atv/atv</italic></td>
<td valign="top" align="left">Breeding</td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left">Pet-3-(p-coumaroyl)-rut-5-glc;<break/> Del-3-rut</td>
<td valign="top" align="left">Peel: 116.11 mg 100 g<sup>&#x2013;1</sup> FW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B130">Mes et al., 2008</xref></td>
</tr>
<tr>
<td valign="top" align="left">Sun Black (<italic>Aft/Aft</italic> &#x00D7; <italic>atv/atv</italic>)</td>
<td valign="top" align="left">Breeding</td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left">Pet-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc;<break/> Mal-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc</td>
<td valign="top" align="left">More than 1 mg g<sup>&#x2013;1</sup> DW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B126">Mazzucato et al., 2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Blue Japan Indigo tomato<break/> (<italic>Aft/Aft</italic> &#x00D7; <italic>atv/atv</italic>)</td>
<td valign="top" align="left">Breeding</td>
<td valign="top" align="left">&#x2014;</td>
<td valign="top" align="left">Pet + p-coumaroyl + rut + glyc;<break/> Mal + p-coumaroyl + rut;<break/> Del</td>
<td valign="top" align="left">Peel: 17 mg g<sup>&#x2013;1</sup> DW<break/> Pulp: 0.1 mg g<sup>&#x2013;1</sup> DW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B139">Ooe et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>Aft/Aft</italic> &#x00D7; <italic>atv/atv</italic> &#x00D7; <italic>hp2/hp2</italic></td>
<td valign="top" align="left">Breeding</td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left">Pet-(p-coumaroyl)-rut-hex;<break/> Del-3-(p-coumaroyl)-rut-glyc;<break/> Pet-(p-coumaroyl)-rut-hex;<break/> Pet-3-(caffeoyl)-rut-5-glyc;<break/> Mal-3-(p-coumaroyl)-rut-5-glyc;<break/> Cya-3-<italic>O</italic>-rut;</td>
<td valign="top" align="left">Peel: 90.91 mg 100 g<sup>&#x2013;1</sup> FW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B37">da Silva Souza et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>ANT1 from S. chilense</italic></td>
<td valign="top" align="left">Genetic engineering</td>
<td valign="top" align="left"><italic>CHS, DFR, 3-GT, 5-GT, GST, ANP</italic></td>
<td valign="top" align="left">Del-3-rut-5-glc;<break/> Del-3-(p-coumaroyl)-rut-glyc;<break/> Del-3-(caffeoyl)-rut-5-glyc;<break/> Pet-3-rut-5-glc;<break/> Pet-3-(p-coumaroyl)-rut-5-glyc;<break/> Pet-3-(caffeoyl)-rut-5-glyc;<break/> Mal-3-rut-5-glc;<break/> Mal-3-(p-coumaryl)-rut-5-glyc;<break/> Mal-3-(caffeoyl)-rut-5-glyc</td>
<td valign="top" align="left">3.574 mg g<sup>&#x2013;1</sup> FW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B125">Mathews et al., 2003</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>Del/Ros1</italic></td>
<td valign="top" align="left">Genetic engineering</td>
<td valign="top" align="left"><italic>PAL, C3H, CHI, F3&#x2032;5&#x2032;H, DFR, ANS, 3-GT, 5-GT, RT, AAC, GST, ANP</italic></td>
<td valign="top" align="left">Pet-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc;<break/> Del-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc;<break/> Pet-3-(feruloyl)-rut-5-glc;<break/> Del-3-(feruloyl)-rut-5-glc</td>
<td valign="top" align="left">2.835 &#x00B1; 0.456 mg g<sup>&#x2013;1</sup> FW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B26">Butelli et al., 2008</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>Del/Ros1</italic></td>
<td valign="top" align="left">Genetic engineering</td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left">Del-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc;<break/> Pet-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc;<break/> Mal-3-(p-coumaroyl)-rut-5-glc;<break/> Mal-3-(feruloyl)-rut-5-glc</td>
<td valign="top" align="left">Peel: 5.1 &#x00B1; 0.5 g kg<sup>&#x2013;1</sup> DW<break/> Flesh: 5.8 &#x00B1; 0.3 g kg<sup>&#x2013;1</sup> DW<break/> Whole fruit: 5.2 &#x00B1; 0.5 g Peo-3-glc equivalent kg<sup>&#x2013;1</sup> DW, or 0.5% of DW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B177">Su et al., 2016</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>ANT1 from S. lycopersicum</italic></td>
<td valign="top" align="left">Genetic engineering</td>
<td valign="top" align="left"><italic>CHI, F3H, DFR, ANS, 3-GT</italic></td>
<td valign="top" align="left">Pet<break/> Mal<break/> Del</td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B165">Schreiber et al., 2012</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>SlANT1</italic> and <italic>SlAN2</italic></td>
<td valign="top" align="left">Genetic engineering</td>
<td valign="top" align="left"><italic>SlAN2, SlANT1, SlAN1, SlAN11, SlJAF13, SlDFR</italic></td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B93">Kiferle et al., 2015</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>Del/Ros1</italic> &#x00D7; <italic>AtMYB12</italic></td>
<td valign="top" align="left">Genetic engineering</td>
<td valign="top" align="left"><italic>PAL, 4CL, CHS, CHI, F3H, FLS, DFR, ANP, 3-GT, C3H</italic></td>
<td valign="top" align="left">Del-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc;<break/> Pet-3-(<italic>trans</italic>-p-coumaroyl)-rut-5-glc;<break/> Pet-3-(feruloyl)-rut-5-glc;<break/> Mal-3-(p-coumaroyl)-rut-5-glc</td>
<td valign="top" align="left">1.154 &#x00B1; 0.011 mg g<sup>&#x2013;1</sup> FW<break/> 2.857 &#x00B1; 0.218 mg g<sup>&#x2013;1</sup> FW<break/> 0.922 &#x00B1; 0.102 mg g<sup>&#x2013;1</sup> FW<break/> 0.598 &#x00B1; 0.011 mg g<sup>&#x2013;1</sup> FW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B213">Zhang et al., 2015</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>SlMYB75</italic></td>
<td valign="top" align="left">Genetic engineering</td>
<td valign="top" align="left"><italic>PAL, CHI, CHS, AAC, ANS, 3-RT, LDOX</italic></td>
<td valign="top" align="left">&#x2013;</td>
<td valign="top" align="left">&#x223C;2 mg g<sup>&#x2013;1</sup> FW</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B88">Jian et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left"><italic>PhAN4</italic></td>
<td valign="top" align="left">Genetic engineering (transformed tomato hairy root cultures)</td>
<td valign="top" align="left"><italic>CHS, CHI, F3&#x2032;5&#x2032;H, F3H LDOX, DFR, ANS, 3-GT, RT, OMT, AAT, ANP, GST</italic></td>
<td valign="top" align="left">Pet-3-(feruloyl)-rut-5-glc;<break/> Pet-3-(p-coumaroyl)-rut-5-glc;<break/> Pel-3glc;<break/> Mal-3-(4-coumaroyl)-rut-5-glc;<break/> Del-3-(p-coumaroyl)-rut-5-glc;<break/> Del-3-5-glc</td>
<td valign="top" align="left">37 &#x03BC;g g<sup>&#x2013;1</sup> DW</td>
<td valign="top" align="left"/></tr>
</tbody>
</table>
<table-wrap-foot>
<fn id="tfn2"><p><italic>The main overexpressed genes and anthocyanins content are shown where available.</italic></p></fn>
<fn id="tfn3"><p><italic>Del, delphinidin; Pet, petunidin; Mal, malvidin; Cya, cyanidin; Peo, peonidin; Pel, pelargonidin; rut, rutinoside; glc, glucoside; glyc, glycoside; hex, hexoside; FW, fresh weight; DW, dry weight.</italic></p></fn>
</table-wrap-foot>
</table-wrap>
<p>Interestingly, the <italic>PhAN4</italic>-related transcriptomic enhancement was found to involve more than 30 genes specifically related to response to biotic/abiotic and oxidative stress, as well. Indeed, GOE analysis was associated with proteinase inhibitors, beta-glucosidases, glucanases, glycosylases, xylan acetylases, resistance proteins, and other classes of enzymes that are players of defense against pathogens and pests and of response to abiotic stresses specifically associated with wounding, cold, heat, drought, hypoxia, and to UV exposure in tomato (<xref ref-type="bibr" rid="B52">Fan et al., 2020</xref>). Among those, the upregulated beta-glucosidases, together with the dirigent proteins and the monoterpenoid and sesquiterpenoid synthases that were found in the present work, are involved in the formation of required intermediates for cell wall lignification. The positive regulation of trichome birefringence-like protein mediating xylan acetylation also is another tool in possible protection against environmental stresses among which there is cold and excess of minerals in the soil. Acetylation of wall polymers is, indeed, vital for plant growth and adaptation to various environments, and is required for the structural integrity of the leaf surface exerting a global impact on plant stress responses (<xref ref-type="bibr" rid="B63">Gao et al., 2017</xref>). In relation to the positive regulation of beta-1,3-glucanases, beta-glucosidases, and xylan acetylases, together with expansions, it has to be added that these genes are related to fruit softening or improved emission of volatiles, as well (<xref ref-type="bibr" rid="B191">Tzin et al., 2015</xref>; <xref ref-type="bibr" rid="B109">Li P. et al., 2020</xref>). In this sense, the positive regulation of chlorophyll a/b binding protein (that is normally upregulated during fruit ripening) and of one gene related to volatile compounds biosynthesis (<italic>chorismate mutase</italic>) was found in <italic>PhAN4</italic> HRCs. At the same time, negative regulation of other genes, which down expression is involved in the extended shelf life of fruits, was found. The evaluation of these aspects might be important in view of the development/design of whole transgenic tomato plants in relation to the quality traits of fruits.</p>
<p>One player of ROS detoxification and regulator of the redox signaling network of tomato, plastidial thioredoxin Y2, was found to be highly upregulated, as well. Moreover, the analysis demonstrated the downregulation of violaxanthin de-epoxidase (<italic>VDE</italic>) and carotenoid isomerase (<italic>CRTISO</italic>), two genes involved in carotenoid biosynthesis. Despite being involved in the photo-inhibition of the PSII, suppression of VDE can induce, at the same time, an accumulation of fucoxanthin that functions as an efficient anti-oxidant in anoxia conditions (<xref ref-type="bibr" rid="B131">Mikami and Hosokawa, 2013</xref>). The downregulation of carotenoid isomerase was demonstrated to induce an accumulation of zeta-carotene and <italic>cis</italic>-prolycopene in tomato fruits (<xref ref-type="bibr" rid="B86">Isaacson et al., 2002</xref>; <xref ref-type="bibr" rid="B147">Pinheiro et al., 2019</xref>), both elevating and modifying carotenoid profiles toward more bioavailable forms compared to wild-type (<xref ref-type="bibr" rid="B34">Cooperstone et al., 2015</xref>). Therefore, the ROS counteracting potential of <italic>PhAN4</italic> HRC material may be related not only to anthocyanins but also to other accumulating anti-oxidant specialized metabolites.</p>
<p>In view of the future development of natural anti-oxidants produced by engineered plants and possibly administered with the diet, and to define whether the significantly higher DPPH antioxidant capacity of specialized metabolites accumulating in <italic>PhAN4</italic> HRCs may be efficiently maintained after ionizing radiation, we exposed lyophilized biomass from AN4-1 HRC to high dose <sup>60</sup>Co gamma radiation. Gamma rays are a component of cosmic ionizing radiation and induce the formation of free radical species (i.e., paramagnetic species). When carried out in an air atmosphere, gamma rays induce the formation of ROS, such as superoxide, peroxide, and hydroxyl radicals, that are responsible for several oxidative processes in biological systems (<xref ref-type="bibr" rid="B121">Marcu et al., 2013b</xref>; <xref ref-type="bibr" rid="B166">Schreurs et al., 2016</xref>). Gamma rays are perfect ROS inducers both directly through water radiolysis, and indirectly <italic>via</italic> the activation of a broad range of signaling processes (e.g., damages to the mitochondria or cell microenvironment) (<xref ref-type="bibr" rid="B155">Riley, 1994</xref>; <xref ref-type="bibr" rid="B11">Azzam et al., 2012</xref>; <xref ref-type="bibr" rid="B27">Buttarelli et al., 2019</xref>). ESR Spectroscopy was used as a sensitive tool to identify the entity of the paramagnetic species generated in the HCRs samples after gamma irradiation (<xref ref-type="bibr" rid="B3">Aleksieva et al., 2009</xref>; <xref ref-type="bibr" rid="B77">Hawkins and Davies, 2014</xref>; <xref ref-type="bibr" rid="B43">D&#x2019;Errico et al., 2018</xref>). ESR analyses revealed a significant difference in the overall amounts of radical species accumulated in the two HRC molecular backgrounds. At the same absorbed dose, control generates a very intense peroxyl radical signal, while a considerably lower level of the singlet intensity is generated in AN4-1. This result reveals that the molecular set formed upon <italic>PhAN4</italic> expression provides very effective free radical scavengers efficiently counteracting oxidative stress upon gamma radiation.</p>
<p>The UV-VIS analysis allowed us to confirm the results obtained by metabolomic data and to characterize the effect of ionizing radiation on the antioxidant compounds. Gamma irradiation, <italic>via</italic> releasing free radicals in solution, may alter these plant constituents (<xref ref-type="bibr" rid="B102">Lateef and Al-Nimer, 2009</xref>; <xref ref-type="bibr" rid="B101">Lalande et al., 2019</xref>). Compared to the substantially unchanged spectra of AN4-1, the absorbance decrease of the 320 nm peak (i.e., flavonols, hydroxycinnamic acids, tannins, flavonols, and anthocyanins associated to caffeic and coumaric acids) controls upon irradiation, suggests that the anthocyanins accumulated in <italic>PhAN4</italic> HRCs are particularly stable to gamma high absorbed dose and probably have protective effects on other biomolecules. Indirectly, this result shows that these molecules may give a major contribution to the ROS buffering capacity under radiation shown by ESR and to the overall antioxidant potential. As a confirmation of the possible significance of this result <italic>in vivo</italic>, it was reported that, even at higher absorbed doses than that used in this work, X rays (e.g., another type of ionizing radiation) leave the level of flavonoids in an aqueous solution unchanged due to the radiolysis-mediated formation of depsides that, in addition, maintain good anti-oxidant properties, as well (<xref ref-type="bibr" rid="B98">Kozlowski et al., 2007</xref>; <xref ref-type="bibr" rid="B102">Lateef and Al-Nimer, 2009</xref>).</p>
<p>For proteins to be functional within a cell requires coordinated folding processes to obtain a correct 3D shape. Disruptions to protein folding, that can occur in space due to ionizing radiation, can have profound biological implications for all organisms, including plant cells, leading to dysfunctions (<xref ref-type="bibr" rid="B17">Blanco et al., 2018</xref>; <xref ref-type="bibr" rid="B101">Lalande et al., 2019</xref>). For this reason, investigations were conducted through photoluminescence analysis on HRCs&#x2019; total soluble protein extracts. When a protein is exposed to the wavelength of 280 nm, mainly the tryptophan and tyrosine residues get excited, which would reflect upon its tertiary structure (<xref ref-type="bibr" rid="B208">Yang H. et al., 2015</xref>). The maximum and emission peak position reflects upon secondary, tertiary, and quaternary structures (<xref ref-type="bibr" rid="B78">Hilaire et al., 2017</xref>). Moreover, the extent of protein oxidation is measured by determining the loss of specific tryptophan fluorescence. The emission spectra of HRCs showed an overall decrease in maximum emission intensities only in the case of irradiated controls, revealing that the structure of soluble proteins is partially lost upon irradiation in those samples. This result demonstrates a low capacity of proteins of control HRCs to counteract unfolding, binding to hydrophobic pockets, and aggregation, witnessed by the loss of fluorescence due to the burial of tryptophan residues after radiation. In particular, the &#x0394;% photoluminescence intensity/mass units after and before irradiation indicated that soluble proteins from control undergo a doubled oxidative stress compared to AN4-1 samples. Being polyphenols emitting at 280 and 320 nm extracted by PBS together with total soluble proteins (anthocyanins are not efficiently extracted, <xref ref-type="supplementary-material" rid="FS3">Supplementary Figure 4</xref>), the contribution of these classes of molecules may be hypothesized in stabilizing proteins, as proofs of the interaction of anthocyanins with proteins seem to suggest (<xref ref-type="bibr" rid="B178">Sui et al., 2018</xref>). Possible additional contributions of enzymatic players to mitigation of misfolding and aggregation <italic>in vivo</italic> may be the object of future studies.</p>
<p>In conclusion, plant biotechnology methods may thus be exploited for the generation of plants capable of dealing with harsh conditions such as those typical of space outposts. MicroTom HRC allowed to rapidly test <italic>PhAN4</italic> expression effects on tomato cells, possibly opening the way to apply to the engineering of whole plants able to perform in a suitable and predictable manner in those environments.</p>
</sec>
<sec sec-type="data-availability" id="S5">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: <ext-link ext-link-type="uri" xlink:href="https://dataview.ncbi.nlm.nih.gov/object/PRJNA794337?reviewer=estprpllasrt3f3libdoij8rco">https://dataview.ncbi.nlm.nih.gov/object/PRJNA794337?reviewer=estprpllasrt3f3libdoij8rco</ext-link>.</p>
</sec>
<sec id="S6">
<title>Author Contributions</title>
<p>SM planned and designed the project, undertook tomato transformation experiments, PCR screening and maintenance of HRCs, and sample preparation for subsequent analysis, as well as wrote the manuscript. RP handled maintenance of HRCs, contributed to sample preparation and transcriptomic data retrieving and interpretation, and contributed to the writing of the manuscript and the preparation of figures. AB performed sequencing read mapping, identification of DEGs and functional annotation, and enrichment pathway analysis of DEGs. HP undertook cDNA library construction and sequencing for transcriptomic analysis. MB contributed to the identification of DEGs and functional annotation of genes. AC and IS performed gamma irradiation experiments, ESR, UV-VIS, and photoluminescence analysis and contributed to writing the manuscript. GD and OD performed MS analysis, anthocyanin identification/quantification, and contributed to writing the manuscript. FP conducted the qPCR analysis. AD and PD performed the Trolox assay and the quantification of total polyphenol content and contributed to writing the manuscript. FQ, RK, and CS assembled and kindly provided the PhAN4 constructs used in this work. ElB contributed to the maintenance of HRCs. EuB reviewed and contributed to the writing of the manuscript. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="conf1" sec-type="COI-statement">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="pudiscl1" sec-type="disclaimer">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
<back>
<sec sec-type="funding-information" id="S7">
<title>Funding</title>
<p>This work was supported by the ENEA/ASI (Italian Space Agency) BIOExTREME and HORTSPACE Projects (ASI n. 2014-007-R.0, ASI n. 2017-11-H.0).</p>
</sec>
<ack>
<p>We are deeply grateful to Stefania Baccaro (Fusion and Nuclear Safety Technologies Department, Casaccia Research Center, Rome, Italy) for enthusiastic support and for sharing precious advice concerning radiation experiments, although premature death did not allow her to see the end of the work. We thank Alessia Fiore (ENEA, BIOTEC) for help in the qualitative analysis of RNAs extracted from HRCs and Giulio Metelli (University of Viterbo/ENEA BIOTEC) for support in collecting data on HRCs growth.</p>
</ack>
<sec id="S9" sec-type="supplementary-material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fpls.2022.830931/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fpls.2022.830931/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Table_1.XLSX" id="TS1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Table 1</label>
<caption><p>Primer identification (id.) as described in &#x201C;Materials and Methods&#x201D; for HRCs PCR screening (for, forward; rev, reverse).</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Presentation_2.PPTX" id="FS1" mimetype="application/vnd.openxmlformats-officedocument.presentationml.presentation" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary File 1</label>
<caption><p>List of figures representing the level of different phenolic compounds and their derivatives in control and <italic>PhAN4</italic> HRCs.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Presentation_3.PPTX" id="FS2" mimetype="application/vnd.openxmlformats-officedocument.presentationml.presentation" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary File 2</label>
<caption><p>List of figures representing the level of different flavonoids in control and PhAN4 HRCs.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Presentation_1.PPTX" id="FS3" mimetype="application/vnd.openxmlformats-officedocument.presentationml.presentation" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary File 3</label>
<caption><p>Complete list of DEGs.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Presentation_1.PPTX" id="FS4" mimetype="application/vnd.openxmlformats-officedocument.presentationml.presentation" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary File 4</label>
<caption><p>GOE analysis results.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Table_2.XLSX" id="TS2" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table_3.DOCX" id="TS3" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
<ref-list>
<title>References</title>
<ref id="B1"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Albert</surname> <given-names>N. W.</given-names></name> <name><surname>Davies</surname> <given-names>K. M.</given-names></name> <name><surname>Lewis</surname> <given-names>D. H.</given-names></name> <name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Montefiori</surname> <given-names>M.</given-names></name> <name><surname>Brendolise</surname> <given-names>C.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in Eudicots.</article-title> <source><italic>Plant Cell</italic></source> <volume>26</volume> <fpage>962</fpage>&#x2013;<lpage>980</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.113.122069</pub-id> <pub-id pub-id-type="pmid">24642943</pub-id></citation></ref>
<ref id="B2"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Albert</surname> <given-names>N. W.</given-names></name> <name><surname>Lewis</surname> <given-names>D. H.</given-names></name> <name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Schwinn</surname> <given-names>K. E.</given-names></name> <name><surname>Jameson</surname> <given-names>P. E.</given-names></name> <name><surname>Davies</surname> <given-names>K. M.</given-names></name></person-group> (<year>2011</year>). <article-title>Members of an R2R3-MYB transcription factor family in Petunia are developmentally and environmentally regulated to control complex floral and vegetative pigmentation patterning.</article-title> <source><italic>Plant J.</italic></source> <volume>65</volume> <fpage>771</fpage>&#x2013;<lpage>784</lpage>. <pub-id pub-id-type="doi">10.1111/j.1365-313X.2010.04465.x</pub-id> <pub-id pub-id-type="pmid">21235651</pub-id></citation></ref>
<ref id="B3"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Aleksieva</surname> <given-names>K.</given-names></name> <name><surname>Georgieva</surname> <given-names>L.</given-names></name> <name><surname>Tzvetkova</surname> <given-names>E.</given-names></name> <name><surname>Yordanov</surname> <given-names>N. D.</given-names></name></person-group> (<year>2009</year>). <article-title>EPR study on tomatoes before and after gamma-irradiation.</article-title> <source><italic>Radiat. Phys. Chem.</italic></source> <volume>78</volume> <fpage>823</fpage>&#x2013;<lpage>825</lpage>. <pub-id pub-id-type="doi">10.1016/j.radphyschem.2009.05.013</pub-id></citation></ref>
<ref id="B4"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Alfenito</surname> <given-names>M. R.</given-names></name> <name><surname>Souer</surname> <given-names>E.</given-names></name> <name><surname>Goodman</surname> <given-names>C. D.</given-names></name> <name><surname>Buell</surname> <given-names>R.</given-names></name> <name><surname>Mol</surname> <given-names>J.</given-names></name> <name><surname>Koes</surname> <given-names>R.</given-names></name><etal/></person-group> (<year>1998</year>). <article-title>Functional complementation of anthocyanin sequestration in the vacuole by widely divergent glutathione S-transferases.</article-title> <source><italic>Plant Cell</italic></source> <volume>10</volume> <fpage>1135</fpage>&#x2013;<lpage>1149</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.10.7.1135</pub-id> <pub-id pub-id-type="pmid">9668133</pub-id></citation></ref>
<ref id="B5"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Amalfitano</surname> <given-names>S.</given-names></name> <name><surname>Levantesi</surname> <given-names>C.</given-names></name> <name><surname>Copetti</surname> <given-names>D.</given-names></name> <name><surname>Stefani</surname> <given-names>F.</given-names></name> <name><surname>Locantore</surname> <given-names>I.</given-names></name> <name><surname>Guarnieri</surname> <given-names>V.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Water and microbial monitoring technologies towards the near future space exploration.</article-title> <source><italic>Water Res.</italic></source> <volume>177</volume>:<issue>115787</issue>. <pub-id pub-id-type="doi">10.1016/j.watres.2020.115787</pub-id> <pub-id pub-id-type="pmid">32315899</pub-id></citation></ref>
<ref id="B6"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ambawat</surname> <given-names>S.</given-names></name> <name><surname>Sharma</surname> <given-names>P.</given-names></name> <name><surname>Yadav</surname> <given-names>N. R.</given-names></name> <name><surname>Yadav</surname> <given-names>R. C.</given-names></name></person-group> (<year>2013</year>). <article-title>MYB transcription factor genes as regulators for plant responses: an overview.</article-title> <source><italic>Phys. Mol. Biol. Plants</italic></source> <volume>19</volume> <fpage>307</fpage>&#x2013;<lpage>321</lpage>. <pub-id pub-id-type="doi">10.1007/s12298-013-0179-1</pub-id> <pub-id pub-id-type="pmid">24431500</pub-id></citation></ref>
<ref id="B7"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Andersen</surname> <given-names>M. L.</given-names></name> <name><surname>Outtrup</surname> <given-names>H.</given-names></name> <name><surname>Skibsted</surname> <given-names>L. H.</given-names></name></person-group> (<year>2000</year>). <article-title>Potential antioxidants in beer assessed by ESR spin trapping.</article-title> <source><italic>J. Agric. Food Chem.</italic></source> <volume>48</volume> <fpage>3106</fpage>&#x2013;<lpage>3111</lpage>. <pub-id pub-id-type="doi">10.1021/jf000354+</pub-id> <pub-id pub-id-type="pmid">10956077</pub-id></citation></ref>
<ref id="B8"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Andolfo</surname> <given-names>G.</given-names></name> <name><surname>Ferriello</surname> <given-names>F.</given-names></name> <name><surname>Tardella</surname> <given-names>L.</given-names></name> <name><surname>Ferrarini</surname> <given-names>A.</given-names></name> <name><surname>Sigillo</surname> <given-names>L.</given-names></name> <name><surname>Frusciante</surname> <given-names>L.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>Tomato genome-wide transcriptional responses to Fusarium wilt and Tomato Mosaic Virus.</article-title> <source><italic>PLoS One</italic></source> <volume>9</volume>:<issue>e94963</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0094963</pub-id> <pub-id pub-id-type="pmid">24804963</pub-id></citation></ref>
<ref id="B9"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Aoki</surname> <given-names>K.</given-names></name> <name><surname>Yano</surname> <given-names>K.</given-names></name> <name><surname>Suzuki</surname> <given-names>A.</given-names></name> <name><surname>Kawamura</surname> <given-names>S.</given-names></name> <name><surname>Sakurai</surname> <given-names>N.</given-names></name> <name><surname>Suda</surname> <given-names>K.</given-names></name><etal/></person-group> (<year>2010</year>). <article-title>Large-scale analysis of full-length cDNA from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.</article-title> <source><italic>BMC Genomics</italic></source> <volume>11</volume>:<issue>210</issue>. <pub-id pub-id-type="doi">10.1186/1471-2164-11-210</pub-id> <pub-id pub-id-type="pmid">20350329</pub-id></citation></ref>
<ref id="B10"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Asins</surname> <given-names>M. J.</given-names></name> <name><surname>Albacete</surname> <given-names>A.</given-names></name> <name><surname>Mart&#x00ED;nez-And&#x00FA;jar</surname> <given-names>C.</given-names></name> <name><surname>Celiktopuz</surname> <given-names>E.</given-names></name> <name><surname>Solmaz</surname> <given-names>&#x0130;</given-names></name> <name><surname>Sar&#x0131;</surname> <given-names>N.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Genetic analysis of root-to-shoot signaling and rootstock-mediated tolerance to water deficit in tomato.</article-title> <source><italic>Genes</italic></source> <volume>12</volume> <fpage>1</fpage>&#x2013;<lpage>25</lpage>. <pub-id pub-id-type="doi">10.3390/genes12010010</pub-id> <pub-id pub-id-type="pmid">33374834</pub-id></citation></ref>
<ref id="B11"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Azzam</surname> <given-names>E. I.</given-names></name> <name><surname>Jay-Gerin</surname> <given-names>J.-P.</given-names></name> <name><surname>Pain</surname> <given-names>D.</given-names></name></person-group> (<year>2012</year>). <article-title>Ionizing radiation-induced metabolic oxidative stress and prolonged cell injury.</article-title> <source><italic>Cancer Lett.</italic></source> <volume>327</volume> <fpage>48</fpage>&#x2013;<lpage>60</lpage>. <pub-id pub-id-type="doi">10.1016/j.canlet.2011.12.012</pub-id> <pub-id pub-id-type="pmid">22182453</pub-id></citation></ref>
<ref id="B12"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Baccaro</surname> <given-names>S.</given-names></name> <name><surname>Cemmi</surname> <given-names>A.</given-names></name> <name><surname>Sarcina</surname> <given-names>I. D.</given-names></name></person-group> (<year>2019</year>). <article-title>Calliope 60 Co gamma irradiation facility for space qualification at ENEA-Casaccia research centre.</article-title> <source><italic>Phys. Astron. Int. J.</italic></source> <volume>3</volume> <fpage>94</fpage>&#x2013;<lpage>100</lpage>. <pub-id pub-id-type="doi">10.15406/paij.2019.03.00164</pub-id></citation></ref>
<ref id="B13"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bendokas</surname> <given-names>V.</given-names></name> <name><surname>Skemiene</surname> <given-names>K.</given-names></name> <name><surname>Trumbeckaite</surname> <given-names>S.</given-names></name> <name><surname>Stanys</surname> <given-names>V.</given-names></name> <name><surname>Passamonti</surname> <given-names>S.</given-names></name> <name><surname>Borutaite</surname> <given-names>V.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Anthocyanins: from plant pigments to health benefits at mitochondrial level.</article-title> <source><italic>Crit. Rev. Food Sci. Nutr.</italic></source> <volume>60</volume> <fpage>3352</fpage>&#x2013;<lpage>3365</lpage>. <pub-id pub-id-type="doi">10.1080/10408398.2019.1687421</pub-id> <pub-id pub-id-type="pmid">31718251</pub-id></citation></ref>
<ref id="B14"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Benjamini</surname> <given-names>Y.</given-names></name> <name><surname>Hochberg</surname> <given-names>Y.</given-names></name></person-group> (<year>1995</year>). <article-title>Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing.</article-title> <source><italic>J. R. Statist. Soc. Ser. B</italic></source> <volume>57</volume> <fpage>289</fpage>&#x2013;<lpage>300</lpage>. <pub-id pub-id-type="doi">10.1111/j.2517-6161.1995.tb02031.x</pub-id></citation></ref>
<ref id="B15"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bergey</surname> <given-names>D. R.</given-names></name> <name><surname>Howe</surname> <given-names>G. A.</given-names></name> <name><surname>Ryan</surname> <given-names>C. A.</given-names></name></person-group> (<year>1996</year>). <article-title>Polypeptide signaling for plant defensive genes exhibits analogies to defense signaling in animals.</article-title> <source><italic>Proc. Natl. Acad. Sci. U. S. A.</italic></source> <volume>93</volume> <fpage>12053</fpage>&#x2013;<lpage>12058</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.93.22.12053</pub-id> <pub-id pub-id-type="pmid">8901530</pub-id></citation></ref>
<ref id="B16"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bijlani</surname> <given-names>S.</given-names></name> <name><surname>Stephens</surname> <given-names>E.</given-names></name> <name><surname>Singh</surname> <given-names>N. K.</given-names></name> <name><surname>Venkateswaran</surname> <given-names>K.</given-names></name> <name><surname>Wang</surname> <given-names>C. C. C.</given-names></name></person-group> (<year>2021</year>). <article-title>Advances in space microbiology.</article-title> <source><italic>Iscience</italic></source> <volume>24</volume>:<issue>102395</issue>. <pub-id pub-id-type="doi">10.1016/j.isci.2021.102395</pub-id> <pub-id pub-id-type="pmid">33997680</pub-id></citation></ref>
<ref id="B17"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Blanco</surname> <given-names>Y.</given-names></name> <name><surname>de Diego-Castilla</surname> <given-names>G.</given-names></name> <name><surname>Vi&#x00FA;dez-Moreiras</surname> <given-names>D.</given-names></name> <name><surname>Cavalcante-Silva</surname> <given-names>E.</given-names></name> <name><surname>Rodr&#x00ED;guez-Manfredi</surname> <given-names>J. A.</given-names></name> <name><surname>Davila</surname> <given-names>A. F.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Effects of Gamma and Electron Radiation on the Structural Integrity of Organic Molecules and Macromolecular Biomarkers Measured by Microarray Immunoassays and Their Astrobiological Implications.</article-title> <source><italic>Astrobiology</italic></source> <volume>18</volume> <fpage>1497</fpage>&#x2013;<lpage>1516</lpage>. <pub-id pub-id-type="doi">10.1089/ast.2016.1645</pub-id> <pub-id pub-id-type="pmid">30070898</pub-id></citation></ref>
<ref id="B18"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Blesso</surname> <given-names>C. N.</given-names></name></person-group> (<year>2019</year>). <article-title>Dietary Anthocyanins and Human Health.</article-title> <source><italic>Nutrients</italic></source> <volume>11</volume> <fpage>10</fpage>&#x2013;<lpage>13</lpage>. <pub-id pub-id-type="doi">10.3390/nu11092107</pub-id> <pub-id pub-id-type="pmid">31491856</pub-id></citation></ref>
<ref id="B19"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bognar</surname> <given-names>E.</given-names></name> <name><surname>Sarszegi</surname> <given-names>Z.</given-names></name> <name><surname>Szabo</surname> <given-names>A.</given-names></name> <name><surname>Debreceni</surname> <given-names>B.</given-names></name> <name><surname>Kalman</surname> <given-names>N.</given-names></name> <name><surname>Tucsek</surname> <given-names>Z.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>Antioxidant and Anti-Inflammatory Effects in RAW264.7 Macrophages of Malvidin, a Major Red Wine Polyphenol.</article-title> <source><italic>PLoS One</italic></source> <volume>8</volume>:<issue>e65355</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0065355</pub-id> <pub-id pub-id-type="pmid">23755222</pub-id></citation></ref>
<ref id="B20"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bongue-Bartelsman</surname> <given-names>M.</given-names></name> <name><surname>O&#x2019;Neill</surname> <given-names>S. D.</given-names></name> <name><surname>Yusen</surname> <given-names>T.</given-names></name> <name><surname>Yoder</surname> <given-names>J. I.</given-names></name></person-group> (<year>1994</year>). <article-title>Characterization of the gene encoding dihydroflavonol 4-reductase in tomato.</article-title> <source><italic>Gene</italic></source> <volume>138</volume> <fpage>153</fpage>&#x2013;<lpage>157</lpage>. <pub-id pub-id-type="doi">10.1016/0378-1119(94)90799-4</pub-id></citation></ref>
<ref id="B21"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bournival</surname> <given-names>B. L.</given-names></name> <name><surname>Scott</surname> <given-names>J. W.</given-names></name> <name><surname>Vallejos</surname> <given-names>C. E.</given-names></name></person-group> (<year>1989</year>). <article-title>An isozyme marker for resistance to race 3 of Fusarium oxysporum f. sp. lycopersici in tomato.</article-title> <source><italic>Theor. Appl. Genet.</italic></source> <volume>78</volume> <fpage>489</fpage>&#x2013;<lpage>494</lpage>. <pub-id pub-id-type="doi">10.1007/BF00290832</pub-id> <pub-id pub-id-type="pmid">24225675</pub-id></citation></ref>
<ref id="B22"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bovy</surname> <given-names>A.</given-names></name> <name><surname>de Vos</surname> <given-names>R.</given-names></name> <name><surname>Kemper</surname> <given-names>M.</given-names></name> <name><surname>Schijlen</surname> <given-names>E.</given-names></name> <name><surname>Almenar Pertejo</surname> <given-names>M.</given-names></name> <name><surname>Muir</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2002</year>). <article-title>High-flavonol tomatoes resulting from the heterologous expression of the maize transcription factor genes LC and C1.</article-title> <source><italic>Plant Cell</italic></source> <volume>14</volume> <fpage>2509</fpage>&#x2013;<lpage>2526</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.004218</pub-id> <pub-id pub-id-type="pmid">12368501</pub-id></citation></ref>
<ref id="B23"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Brito</surname> <given-names>A.</given-names></name> <name><surname>Areche</surname> <given-names>C.</given-names></name> <name><surname>Sep&#x00FA;lveda</surname> <given-names>B.</given-names></name> <name><surname>Kennelly</surname> <given-names>E. J.</given-names></name> <name><surname>Simirgiotis</surname> <given-names>M. J.</given-names></name></person-group> (<year>2014</year>). <article-title>Anthocyanin characterization, total phenolic quantification and antioxidant features of some chilean edible berry extracts.</article-title> <source><italic>Molecules</italic></source> <volume>19</volume> <fpage>10936</fpage>&#x2013;<lpage>10955</lpage>. <pub-id pub-id-type="doi">10.3390/molecules190810936</pub-id> <pub-id pub-id-type="pmid">25072199</pub-id></citation></ref>
<ref id="B24"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Brunetti</surname> <given-names>C.</given-names></name> <name><surname>di Ferdinando</surname> <given-names>M.</given-names></name> <name><surname>Fini</surname> <given-names>A.</given-names></name> <name><surname>Pollastri</surname> <given-names>S.</given-names></name> <name><surname>Tattini</surname> <given-names>M.</given-names></name></person-group> (<year>2013</year>). <article-title>Flavonoids as antioxidants and developmental regulators: relative significance in plants and humans.</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>14</volume> <fpage>3540</fpage>&#x2013;<lpage>3555</lpage>. <pub-id pub-id-type="doi">10.3390/ijms14023540</pub-id> <pub-id pub-id-type="pmid">23434657</pub-id></citation></ref>
<ref id="B25"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Buoso</surname> <given-names>S.</given-names></name> <name><surname>Pagliari</surname> <given-names>L.</given-names></name> <name><surname>Musetti</surname> <given-names>R.</given-names></name> <name><surname>Martini</surname> <given-names>M.</given-names></name> <name><surname>Marroni</surname> <given-names>F.</given-names></name> <name><surname>Schmidt</surname> <given-names>W.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>&#x201C;Candidatus phytoplasma solani&#x201D; interferes with the distribution and uptake of iron in tomato.</article-title> <source><italic>BMC Genomics</italic></source> <volume>20</volume>:<issue>703</issue>. <pub-id pub-id-type="doi">10.1186/s12864-019-6062-x</pub-id> <pub-id pub-id-type="pmid">31500568</pub-id></citation></ref>
<ref id="B26"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Butelli</surname> <given-names>E.</given-names></name> <name><surname>Titta</surname> <given-names>L.</given-names></name> <name><surname>Giorgio</surname> <given-names>M.</given-names></name> <name><surname>Mock</surname> <given-names>H. P.</given-names></name> <name><surname>Matros</surname> <given-names>A.</given-names></name> <name><surname>Peterek</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2008</year>). <article-title>Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors.</article-title> <source><italic>Nat. Biotechnol.</italic></source> <volume>26</volume> <fpage>1301</fpage>&#x2013;<lpage>1308</lpage>. <pub-id pub-id-type="doi">10.1038/nbt.1506</pub-id> <pub-id pub-id-type="pmid">18953354</pub-id></citation></ref>
<ref id="B27"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Buttarelli</surname> <given-names>M.</given-names></name> <name><surname>Babini</surname> <given-names>G.</given-names></name> <name><surname>Raspaglio</surname> <given-names>G.</given-names></name> <name><surname>Filippetti</surname> <given-names>F.</given-names></name> <name><surname>Battaglia</surname> <given-names>A.</given-names></name> <name><surname>Ciucci</surname> <given-names>A.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>A combined ANXA2-NDRG1-STAT1 gene signature predicts response to chemoradiotherapy in cervical cancer.</article-title> <source><italic>J. Exp. Clin. Cancer Res.</italic></source> <volume>38</volume>:<issue>279</issue>.</citation></ref>
<ref id="B28"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cao</surname> <given-names>X.</given-names></name> <name><surname>Qiu</surname> <given-names>Z.</given-names></name> <name><surname>Wang</surname> <given-names>X.</given-names></name> <name><surname>van Giang</surname> <given-names>T.</given-names></name> <name><surname>Liu</surname> <given-names>X.</given-names></name> <name><surname>Wang</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>A putative R3 MYB repressor is the candidate gene underlying atroviolacium, a locus for anthocyanin pigmentation in tomato fruit.</article-title> <source><italic>J. Exp. Bot.</italic></source> <volume>68</volume> <fpage>5745</fpage>&#x2013;<lpage>5758</lpage>. <pub-id pub-id-type="doi">10.1093/jxb/erx382</pub-id> <pub-id pub-id-type="pmid">29186488</pub-id></citation></ref>
<ref id="B29"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Carmona</surname> <given-names>L.</given-names></name> <name><surname>Alqu&#x00E9;zar</surname> <given-names>B.</given-names></name> <name><surname>Diretto</surname> <given-names>G.</given-names></name> <name><surname>Sevi</surname> <given-names>F.</given-names></name> <name><surname>Malara</surname> <given-names>T.</given-names></name> <name><surname>Lafuente</surname> <given-names>M. T.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Curing and low-temperature combined post-harvest storage enhances anthocyanin biosynthesis in blood oranges.</article-title> <source><italic>Food Chem.</italic></source> <volume>342</volume>:<issue>128334</issue>. <pub-id pub-id-type="doi">10.1016/j.foodchem.2020.128334</pub-id> <pub-id pub-id-type="pmid">33077281</pub-id></citation></ref>
<ref id="B30"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cock</surname> <given-names>P. J. A.</given-names></name> <name><surname>Fields</surname> <given-names>C. J.</given-names></name> <name><surname>Goto</surname> <given-names>N.</given-names></name> <name><surname>Heuer</surname> <given-names>M. L.</given-names></name> <name><surname>Rice</surname> <given-names>P. M.</given-names></name></person-group> (<year>2009</year>). <article-title>The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>38</volume> <fpage>1767</fpage>&#x2013;<lpage>1771</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkp1137</pub-id> <pub-id pub-id-type="pmid">20015970</pub-id></citation></ref>
<ref id="B31"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Colanero</surname> <given-names>S.</given-names></name> <name><surname>Perata</surname> <given-names>P.</given-names></name> <name><surname>Gonzali</surname> <given-names>S.</given-names></name></person-group> (<year>2020</year>). <article-title>What&#x2019;s behind Purple Tomatoes? Insight into the Mechanisms of Anthocyanin Synthesis in Tomato Fruits.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>182</volume> <fpage>1841</fpage>&#x2013;<lpage>1853</lpage>. <pub-id pub-id-type="doi">10.1104/pp.19.01530</pub-id> <pub-id pub-id-type="pmid">31980573</pub-id></citation></ref>
<ref id="B32"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Conconi</surname> <given-names>A.</given-names></name> <name><surname>Smerdon</surname> <given-names>M. J.</given-names></name> <name><surname>Howe</surname> <given-names>G. A.</given-names></name> <name><surname>Ryan</surname> <given-names>C. A.</given-names></name></person-group> (<year>1996</year>). <article-title>The octadecanoid signalling pathway in plants mediates Response To Ultraviolet Radiation.</article-title> <source><italic>Nature</italic></source> <volume>383</volume> <fpage>826</fpage>&#x2013;<lpage>829</lpage>.</citation></ref>
<ref id="B33"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Consortium</surname> <given-names>T. T. G.</given-names></name> <name><surname>Sato</surname> <given-names>S.</given-names></name> <name><surname>Tabata</surname> <given-names>S.</given-names></name> <name><surname>Hirakawa</surname> <given-names>H.</given-names></name> <name><surname>Asamizu</surname> <given-names>E.</given-names></name> <name><surname>Shirasawa</surname> <given-names>K.</given-names></name><etal/></person-group> (<year>2012</year>). <article-title>The tomato genome sequence provides insights into fleshy fruit evolution.</article-title> <source><italic>Nature</italic></source> <volume>485</volume>:<issue>635</issue>. <pub-id pub-id-type="doi">10.1038/nature11119</pub-id> <pub-id pub-id-type="pmid">22660326</pub-id></citation></ref>
<ref id="B34"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cooperstone</surname> <given-names>J. L.</given-names></name> <name><surname>Ralston</surname> <given-names>R. A.</given-names></name> <name><surname>Riedl</surname> <given-names>K. M.</given-names></name> <name><surname>Haufe</surname> <given-names>T. C.</given-names></name> <name><surname>Ralf</surname> <given-names>M.</given-names></name></person-group> (<year>2015</year>). <article-title>Enhanced bioavailability of lycopene when consumed as cis-isomers from tangerine compared to red tomato juice, a randomized, cross-over clinical trial.</article-title> <source><italic>Mol. Nutr. Food Res.</italic></source> <volume>59</volume> <fpage>658</fpage>&#x2013;<lpage>669</lpage>. <pub-id pub-id-type="doi">10.1002/mnfr.201400658</pub-id> <pub-id pub-id-type="pmid">25620547</pub-id></citation></ref>
<ref id="B35"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Copp</surname> <given-names>R. R.</given-names></name> <name><surname>Peebles</surname> <given-names>D. D.</given-names></name> <name><surname>Soref</surname> <given-names>C. M.</given-names></name> <name><surname>Fahl</surname> <given-names>W. E.</given-names></name></person-group> (<year>2013</year>). <article-title>Radioprotective efficacy and toxicity of a new family of aminothiol analogs.</article-title> <source><italic>Int. J. Radiat. Biol.</italic></source> <volume>89</volume> <fpage>485</fpage>&#x2013;<lpage>492</lpage>. <pub-id pub-id-type="doi">10.3109/09553002.2013.770579</pub-id> <pub-id pub-id-type="pmid">23369131</pub-id></citation></ref>
<ref id="B36"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>da Silva</surname> <given-names>F. L.</given-names></name> <name><surname>Escribano-Bail&#x00F3;n</surname> <given-names>M. T.</given-names></name> <name><surname>P&#x00E9;rez Alonso</surname> <given-names>J. J.</given-names></name> <name><surname>Rivas-Gonzalo</surname> <given-names>J. C.</given-names></name> <name><surname>Santos-Buelga</surname> <given-names>C.</given-names></name></person-group> (<year>2007</year>). <article-title>Anthocyanin pigments in strawberry.</article-title> <source><italic>LWT Food Sci. Technol.</italic></source> <volume>40</volume> <fpage>374</fpage>&#x2013;<lpage>382</lpage>. <pub-id pub-id-type="doi">10.1016/j.lwt.2005.09.018</pub-id></citation></ref>
<ref id="B37"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>da Silva Souza</surname> <given-names>M. A.</given-names></name> <name><surname>Peres</surname> <given-names>L. E. P.</given-names></name> <name><surname>Freschi</surname> <given-names>J. R.</given-names></name> <name><surname>Purgatto</surname> <given-names>E.</given-names></name> <name><surname>Lajolo</surname> <given-names>F. M.</given-names></name> <name><surname>Hassimotto</surname> <given-names>N. M. A.</given-names></name></person-group> (<year>2020</year>). <article-title>Changes in flavonoid and carotenoid profiles alter volatile organic compounds in purple and orange cherry tomatoes obtained by allele introgression.</article-title> <source><italic>J. Sci. Food Agric.</italic></source> <volume>100</volume> <fpage>1662</fpage>&#x2013;<lpage>1670</lpage>. <pub-id pub-id-type="doi">10.1002/jsfa.10180</pub-id> <pub-id pub-id-type="pmid">31808163</pub-id></citation></ref>
<ref id="B38"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Daly</surname> <given-names>S.</given-names></name> <name><surname>Bianchini</surname> <given-names>R.</given-names></name> <name><surname>Polefka</surname> <given-names>T.</given-names></name> <name><surname>Jumbelic</surname> <given-names>L.</given-names></name> <name><surname>Jachowicz</surname> <given-names>J.</given-names></name></person-group> (<year>2009</year>). <article-title>Fluorescence and coloration of grey hair.</article-title> <source><italic>Int. J. Cosmet. Sci.</italic></source> <volume>31</volume> <fpage>347</fpage>&#x2013;<lpage>359</lpage>. <pub-id pub-id-type="doi">10.1111/j.1468-2494.2009.00500.x</pub-id> <pub-id pub-id-type="pmid">19723161</pub-id></citation></ref>
<ref id="B39"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>de Ollas</surname> <given-names>C.</given-names></name> <name><surname>Gonz&#x00E1;lez-Guzm&#x00E1;n</surname> <given-names>M.</given-names></name> <name><surname>Pitarch</surname> <given-names>Z.</given-names></name> <name><surname>Matus</surname> <given-names>J. T.</given-names></name> <name><surname>Candela</surname> <given-names>H.</given-names></name> <name><surname>Rambla</surname> <given-names>J. L.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill).</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>12</volume>:<issue>613059</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2021.613059</pub-id> <pub-id pub-id-type="pmid">33746996</pub-id></citation></ref>
<ref id="B40"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>de Torre</surname> <given-names>M. P.</given-names></name> <name><surname>Cavero</surname> <given-names>R. Y.</given-names></name> <name><surname>Calvo</surname> <given-names>M. I.</given-names></name> <name><surname>Vizmanos</surname> <given-names>J. L. W.</given-names></name></person-group> (<year>2019</year>). <article-title>A simple and a reliable method to quantify antioxidant activity <italic>in vivo</italic>.</article-title> <source><italic>Antioxidants</italic></source> <volume>8</volume> <fpage>1</fpage>&#x2013;<lpage>11</lpage>. <pub-id pub-id-type="doi">10.3390/antiox8050142</pub-id> <pub-id pub-id-type="pmid">31121854</pub-id></citation></ref>
<ref id="B41"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>de Vetten</surname> <given-names>N.</given-names></name> <name><surname>ter Horst</surname> <given-names>J.</given-names></name> <name><surname>van Schaik</surname> <given-names>H. P.</given-names></name> <name><surname>de Boer</surname> <given-names>A.</given-names></name> <name><surname>Mol</surname> <given-names>J.</given-names></name> <name><surname>Koes</surname> <given-names>R.</given-names></name></person-group> (<year>1999</year>). <article-title>A cytochrome b5 is required for full activity of flavonoid 3&#x2032;,5&#x2032;-hydroxylase, a cytochrome P450 involved in the formation of blue flower colors.</article-title> <source><italic>Proc. Natl. Acad. Sci. U. S. A.</italic></source> <volume>96</volume> <fpage>778</fpage>&#x2013;<lpage>783</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.96.2.778</pub-id> <pub-id pub-id-type="pmid">9892710</pub-id></citation></ref>
<ref id="B42"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>de Vries</surname> <given-names>J.</given-names></name> <name><surname>Archibald</surname> <given-names>J. M.</given-names></name></person-group> (<year>2018</year>). <article-title>Plant evolution: landmarks on the path to terrestrial life.</article-title> <source><italic>New Phytol.</italic></source> <volume>217</volume> <fpage>1428</fpage>&#x2013;<lpage>1434</lpage>. <pub-id pub-id-type="doi">10.1111/nph.14975</pub-id> <pub-id pub-id-type="pmid">29318635</pub-id></citation></ref>
<ref id="B43"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>D&#x2019;Errico</surname> <given-names>G.</given-names></name> <name><surname>Vitiello</surname> <given-names>G.</given-names></name> <name><surname>de Tommaso</surname> <given-names>G.</given-names></name> <name><surname>Abdel-Gawad</surname> <given-names>F. K.</given-names></name> <name><surname>Brundo</surname> <given-names>M. V.</given-names></name> <name><surname>Ferrante</surname> <given-names>M.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Electron Spin Resonance (ESR) for the study of Reactive Oxygen Species (ROS) on the isolated frog skin (Pelophylax bergeri): a non-invasive method for environmental monitoring.</article-title> <source><italic>Environ. Res.</italic></source> <volume>165</volume> <fpage>11</fpage>&#x2013;<lpage>18</lpage>. <pub-id pub-id-type="doi">10.1016/j.envres.2018.03.044</pub-id> <pub-id pub-id-type="pmid">29655038</pub-id></citation></ref>
<ref id="B44"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Desiderio</surname> <given-names>A.</given-names></name> <name><surname>Salzano</surname> <given-names>A. M.</given-names></name> <name><surname>Scaloni</surname> <given-names>A.</given-names></name> <name><surname>Massa</surname> <given-names>S.</given-names></name> <name><surname>Pimpinella</surname> <given-names>M.</given-names></name> <name><surname>de Coste</surname> <given-names>V.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Effects of Simulated Space Radiations on the Tomato Root Proteome.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>10</volume>:<issue>1334</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2019.01334</pub-id> <pub-id pub-id-type="pmid">31708949</pub-id></citation></ref>
<ref id="B45"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>DeZwart</surname> <given-names>M.</given-names></name> <name><surname>Henderson</surname> <given-names>S.</given-names></name></person-group> (<year>2021</year>). <source><italic>Commercial and Military Uses of Outer Space.</italic></source> <publisher-loc>Germany</publisher-loc>: <publisher-name>Springer</publisher-name>.</citation></ref>
<ref id="B46"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Diretto</surname> <given-names>G.</given-names></name> <name><surname>Jin</surname> <given-names>X.</given-names></name> <name><surname>Capell</surname> <given-names>T.</given-names></name> <name><surname>Zhu</surname> <given-names>C.</given-names></name> <name><surname>Gomez-Gomez</surname> <given-names>L.</given-names></name></person-group> (<year>2019</year>). <article-title>Differential accumulation of pelargonidin glycosides in petals at three different developmental stages of the orange-flowered gentian (Gentiana lutea L. var. aurantiaca).</article-title> <source><italic>PLoS One</italic></source> <volume>14</volume>:<issue>e0212062</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0212062</pub-id> <pub-id pub-id-type="pmid">30742659</pub-id></citation></ref>
<ref id="B47"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Dobin</surname> <given-names>A.</given-names></name> <name><surname>Davis</surname> <given-names>C. A.</given-names></name> <name><surname>Schlesinger</surname> <given-names>F.</given-names></name> <name><surname>Drenkow</surname> <given-names>J.</given-names></name> <name><surname>Zaleski</surname> <given-names>C.</given-names></name> <name><surname>Jha</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>STAR: ultrafast universal RNA-seq aligner.</article-title> <source><italic>Bioinformatics</italic></source> <volume>29</volume> <fpage>15</fpage>&#x2013;<lpage>21</lpage>. <pub-id pub-id-type="doi">10.1093/bioinformatics/bts635</pub-id> <pub-id pub-id-type="pmid">23104886</pub-id></citation></ref>
<ref id="B48"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>dos Santos</surname> <given-names>A. L.</given-names></name> <name><surname>Chaves-Silva</surname> <given-names>S.</given-names></name> <name><surname>Yang</surname> <given-names>L.</given-names></name> <name><surname>Maia</surname> <given-names>L. G. S.</given-names></name> <name><surname>Chalfun-J&#x00FA;nior</surname> <given-names>A.</given-names></name> <name><surname>Sinharoy</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Global analysis of the MATE gene family of metabolite transporters in tomato.</article-title> <source><italic>BMC Plant Biol.</italic></source> <volume>17</volume>:<issue>185</issue>. <pub-id pub-id-type="doi">10.1186/s12870-017-1115-2</pub-id> <pub-id pub-id-type="pmid">29084510</pub-id></citation></ref>
<ref id="B49"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Esatbeyoglu</surname> <given-names>T.</given-names></name> <name><surname>Wagner</surname> <given-names>A. E.</given-names></name> <name><surname>Motafakkerazad</surname> <given-names>R.</given-names></name> <name><surname>Nakajima</surname> <given-names>Y.</given-names></name> <name><surname>Matsugo</surname> <given-names>S.</given-names></name> <name><surname>Rimbach</surname> <given-names>G.</given-names></name></person-group> (<year>2014</year>). <article-title>Free radical scavenging and antioxidant activity of betanin: electron spin resonance spectroscopy studies and studies in cultured cells.</article-title> <source><italic>Food Chem. Toxicol.</italic></source> <volume>73</volume> <fpage>119</fpage>&#x2013;<lpage>126</lpage>. <pub-id pub-id-type="doi">10.1016/j.fct.2014.08.007</pub-id> <pub-id pub-id-type="pmid">25152328</pub-id></citation></ref>
<ref id="B50"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fahim</surname> <given-names>S.</given-names></name> <name><surname>Hussein</surname> <given-names>W.</given-names></name> <name><surname>Awad</surname> <given-names>H.</given-names></name></person-group> (<year>2016</year>). <article-title>Systemic Resistance Induction of Tomato Plants against ToMV Virus by Surfactin Produced from Bacillus subtilis BMG02.</article-title> <source><italic>Am. J. of Microbiol. Res.</italic></source> <volume>4</volume> <fpage>153</fpage>&#x2013;<lpage>158</lpage>. <pub-id pub-id-type="doi">10.12691/ajmr-4-5-5</pub-id></citation></ref>
<ref id="B51"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fan</surname> <given-names>K. T.</given-names></name> <name><surname>Hsu</surname> <given-names>Y.</given-names></name> <name><surname>Yeh</surname> <given-names>C. F.</given-names></name> <name><surname>Chang</surname> <given-names>C. H.</given-names></name> <name><surname>Chang</surname> <given-names>W. H.</given-names></name> <name><surname>Chen</surname> <given-names>Y. R.</given-names></name></person-group> (<year>2021</year>). <article-title>Quantitative proteomics reveals the dynamic regulation of the tomato proteome in response to phytophthora infestans.</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>22</volume>:<issue>4174</issue>. <pub-id pub-id-type="doi">10.3390/ijms22084174</pub-id> <pub-id pub-id-type="pmid">33920680</pub-id></citation></ref>
<ref id="B52"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fan</surname> <given-names>Y.</given-names></name> <name><surname>Yang</surname> <given-names>W.</given-names></name> <name><surname>Yan</surname> <given-names>Q.</given-names></name> <name><surname>Chen</surname> <given-names>C.</given-names></name> <name><surname>Li</surname> <given-names>J.</given-names></name></person-group> (<year>2020</year>). <article-title>Genome-Wide Identification and Expression Analysis.</article-title> <source><italic>Genes</italic></source> <volume>11</volume>:<issue>1</issue>.</citation></ref>
<ref id="B53"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fang</surname> <given-names>J.</given-names></name></person-group> (<year>2014</year>). <article-title>Some anthocyanins could be efficiently absorbed across the gastrointestinal mucosa: extensive presystemic metabolism reduces apparent bioavailability.</article-title> <source><italic>J. Agric. Food Chem.</italic></source> <volume>62</volume> <fpage>3904</fpage>&#x2013;<lpage>3911</lpage>. <pub-id pub-id-type="doi">10.1021/jf405356b</pub-id> <pub-id pub-id-type="pmid">24650097</pub-id></citation></ref>
<ref id="B54"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Faraco</surname> <given-names>M.</given-names></name> <name><surname>Spelt</surname> <given-names>C.</given-names></name> <name><surname>Bliek</surname> <given-names>M.</given-names></name> <name><surname>Verweij</surname> <given-names>W.</given-names></name> <name><surname>Hoshino</surname> <given-names>A.</given-names></name> <name><surname>Espen</surname> <given-names>L.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>Hyperacidification of Vacuoles by the Combined Action of Two Different P-ATPases in the Tonoplast Determines Flower Color.</article-title> <source><italic>Cell Rep.</italic></source> <volume>6</volume> <fpage>32</fpage>&#x2013;<lpage>43</lpage>. <pub-id pub-id-type="doi">10.1016/j.celrep.2013.12.009</pub-id> <pub-id pub-id-type="pmid">24388746</pub-id></citation></ref>
<ref id="B55"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Faure</surname> <given-names>A. M.</given-names></name> <name><surname>S&#x00E1;nchez-Ferrer</surname> <given-names>A.</given-names></name> <name><surname>Zabara</surname> <given-names>A.</given-names></name> <name><surname>Andersen</surname> <given-names>M. L.</given-names></name> <name><surname>Nystr&#x00F6;m</surname> <given-names>L.</given-names></name></person-group> (<year>2014</year>). <article-title>Modulating the structural properties of &#x03B2;-d-glucan degradation products by alternative reaction pathways.</article-title> <source><italic>Carbohydrate Polym.</italic></source> <volume>99</volume> <fpage>679</fpage>&#x2013;<lpage>686</lpage>. <pub-id pub-id-type="doi">10.1016/j.carbpol.2013.08.022</pub-id> <pub-id pub-id-type="pmid">24274558</pub-id></citation></ref>
<ref id="B56"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fedenko</surname> <given-names>V. S.</given-names></name> <name><surname>Shemet</surname> <given-names>S. A.</given-names></name> <name><surname>Landi</surname> <given-names>M.</given-names></name></person-group> (<year>2017</year>). <article-title>UV&#x2013;vis spectroscopy and colorimetric models for detecting anthocyanin-metal complexes in plants: an overview of <italic>in vitro</italic> and <italic>in vivo</italic> techniques.</article-title> <source><italic>J. Plant Physiol.</italic></source> <volume>212</volume> <fpage>13</fpage>&#x2013;<lpage>28</lpage>. <pub-id pub-id-type="doi">10.1016/j.jplph.2017.02.001</pub-id> <pub-id pub-id-type="pmid">28242414</pub-id></citation></ref>
<ref id="B57"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fernandez-Moreno</surname> <given-names>J.-P.</given-names></name> <name><surname>Tzfadia</surname> <given-names>O.</given-names></name> <name><surname>Forment</surname> <given-names>J.</given-names></name> <name><surname>Presa</surname> <given-names>S.</given-names></name> <name><surname>Rogachev</surname> <given-names>I.</given-names></name> <name><surname>Meir</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Characterization of a New Pink-Fruited Tomato Mutant Results in the Identification of a Null Allele of the SlMYB12 Transcription Factor.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>171</volume> <fpage>1821</fpage>&#x2013;<lpage>1836</lpage>.</citation></ref>
<ref id="B58"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fernandez-Pozo</surname> <given-names>N.</given-names></name> <name><surname>Menda</surname> <given-names>N.</given-names></name> <name><surname>Edwards</surname> <given-names>J. D.</given-names></name> <name><surname>Saha</surname> <given-names>S.</given-names></name> <name><surname>Tecle</surname> <given-names>I. Y.</given-names></name> <name><surname>Strickler</surname> <given-names>S. R.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>The Sol Genomics Network (SGN)-from genotype to phenotype to breeding.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>43</volume> <fpage>D1036</fpage>&#x2013;<lpage>D1041</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gku1195</pub-id> <pub-id pub-id-type="pmid">25428362</pub-id></citation></ref>
<ref id="B59"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Filiz</surname> <given-names>E.</given-names></name> <name><surname>Cetin</surname> <given-names>D.</given-names></name> <name><surname>Akbudak</surname> <given-names>M. A.</given-names></name></person-group> (<year>2019</year>). <article-title>Aromatic amino acids biosynthesis genes identification and expression analysis under salt and drought stresses in Solanum lycopersicum L.</article-title> <source><italic>Sci. Hortic.</italic></source> <volume>250</volume> <fpage>127</fpage>&#x2013;<lpage>137</lpage>. <pub-id pub-id-type="doi">10.1016/j.scienta.2019.02.044</pub-id></citation></ref>
<ref id="B60"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Florio</surname> <given-names>F. E.</given-names></name> <name><surname>Gattolin</surname> <given-names>S.</given-names></name> <name><surname>Toppino</surname> <given-names>L.</given-names></name> <name><surname>Bassolino</surname> <given-names>L.</given-names></name> <name><surname>Fibiani</surname> <given-names>M.</given-names></name> <name><surname>Scalzo</surname> <given-names>R. L.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>A SmelAAT Acyltransferase Variant Causes a Major Difference in Eggplant (<italic>Solanum melongena</italic> L.) Peel Anthocyanin Composition.</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>22</volume>:9174.</citation></ref>
<ref id="B61"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fu</surname> <given-names>Y.</given-names></name> <name><surname>Li</surname> <given-names>L.</given-names></name> <name><surname>Xie</surname> <given-names>B.</given-names></name> <name><surname>Dong</surname> <given-names>C.</given-names></name> <name><surname>Wang</surname> <given-names>M.</given-names></name> <name><surname>Jia</surname> <given-names>B.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>How to establish a bioregenerative life support system for long-term crewed missions to the moon or mars.</article-title> <source><italic>Astrobiology</italic></source> <volume>16</volume> <fpage>925</fpage>&#x2013;<lpage>936</lpage>. <pub-id pub-id-type="doi">10.1089/ast.2016.1477</pub-id> <pub-id pub-id-type="pmid">27912029</pub-id></citation></ref>
<ref id="B62"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gakamsky</surname> <given-names>A.</given-names></name> <name><surname>Duncan</surname> <given-names>R. R.</given-names></name> <name><surname>Howarth</surname> <given-names>N. M.</given-names></name> <name><surname>Dhillon</surname> <given-names>B.</given-names></name> <name><surname>Buttensch&#x00F6;n</surname> <given-names>K. K.</given-names></name> <name><surname>Daly</surname> <given-names>D. J.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Tryptophan and Non-Tryptophan Fluorescence of the Eye Lens Proteins Provides Diagnostics of Cataract at the Molecular Level.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>7</volume> <fpage>1</fpage>&#x2013;<lpage>15</lpage>. <pub-id pub-id-type="doi">10.1038/srep40375</pub-id> <pub-id pub-id-type="pmid">28071717</pub-id></citation></ref>
<ref id="B63"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gao</surname> <given-names>Y.</given-names></name> <name><surname>He</surname> <given-names>C.</given-names></name> <name><surname>Zhang</surname> <given-names>D.</given-names></name> <name><surname>Liu</surname> <given-names>X.</given-names></name> <name><surname>Xu</surname> <given-names>Z.</given-names></name> <name><surname>Tian</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Two trichome birefringence-like proteins mediate xylan acetylation, which is essential for leaf blight resistance in rice.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>173</volume> <fpage>470</fpage>&#x2013;<lpage>481</lpage>. <pub-id pub-id-type="doi">10.1104/pp.16.01618</pub-id> <pub-id pub-id-type="pmid">27864442</pub-id></citation></ref>
<ref id="B64"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gao</surname> <given-names>Y.</given-names></name> <name><surname>Liu</surname> <given-names>J.</given-names></name> <name><surname>Chen</surname> <given-names>Y.</given-names></name> <name><surname>Tang</surname> <given-names>H.</given-names></name> <name><surname>Wang</surname> <given-names>Y.</given-names></name> <name><surname>He</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Tomato SlAN11 regulates flavonoid biosynthesis and seed dormancy by interaction with bHLH proteins but not with MYB proteins.</article-title> <source><italic>Hortic. Res.</italic></source> <volume>5</volume>:<issue>27</issue>. <pub-id pub-id-type="doi">10.1038/s41438-018-0032-3</pub-id> <pub-id pub-id-type="pmid">29872532</pub-id></citation></ref>
<ref id="B65"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Garg</surname> <given-names>M.</given-names></name> <name><surname>Sharma</surname> <given-names>N.</given-names></name> <name><surname>Sharma</surname> <given-names>S.</given-names></name> <name><surname>Kapoor</surname> <given-names>P.</given-names></name> <name><surname>Kumar</surname> <given-names>A.</given-names></name> <name><surname>Chunduri</surname> <given-names>V.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Biofortified Crops Generated by Breeding, Agronomy, and Transgenic Approaches Are Improving Lives of Millions of People around the World.</article-title> <source><italic>Front. Nutr.</italic></source> <volume>5</volume>:<issue>12</issue>. <pub-id pub-id-type="doi">10.3389/fnut.2018.00012</pub-id> <pub-id pub-id-type="pmid">29492405</pub-id></citation></ref>
<ref id="B66"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gerszberg</surname> <given-names>A.</given-names></name> <name><surname>Hnatuszko-Konka</surname> <given-names>K.</given-names></name> <name><surname>Kowalczyk</surname> <given-names>T.</given-names></name> <name><surname>Kononowicz</surname> <given-names>A. K.</given-names></name></person-group> (<year>2015</year>). <article-title>Tomato (Solanum lycopersicum L.) in the service of biotechnology.</article-title> <source><italic>Plant Cell Tissue Organ Cult.</italic></source> <volume>120</volume> <fpage>881</fpage>&#x2013;<lpage>902</lpage>. <pub-id pub-id-type="doi">10.1007/s11240-014-0664-4</pub-id></citation></ref>
<ref id="B67"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Giovannoni</surname> <given-names>J.</given-names></name></person-group> (<year>2018</year>). <article-title>Tomato Multiomics Reveals Consequences of Crop Domestication and Improvement.</article-title> <source><italic>Cell</italic></source> <volume>172</volume> <fpage>6</fpage>&#x2013;<lpage>8</lpage>. <pub-id pub-id-type="doi">10.1016/j.cell.2017.12.036</pub-id> <pub-id pub-id-type="pmid">29328921</pub-id></citation></ref>
<ref id="B68"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>G&#x00F3;mez</surname> <given-names>X.</given-names></name> <name><surname>Sanon</surname> <given-names>S.</given-names></name> <name><surname>Zambrano</surname> <given-names>K.</given-names></name> <name><surname>Asquel</surname> <given-names>S.</given-names></name> <name><surname>Bassantes</surname> <given-names>M.</given-names></name> <name><surname>Morales</surname> <given-names>J. E.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Key points for the development of antioxidant cocktails to prevent cellular stress and damage caused by reactive oxygen species (ROS) during manned space missions.</article-title> <source><italic>NPJ Microgravity</italic></source> <volume>7</volume> <issue>35</issue>. <pub-id pub-id-type="doi">10.1038/s41526-021-00162-8</pub-id> <pub-id pub-id-type="pmid">34556658</pub-id></citation></ref>
<ref id="B69"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gonzalez</surname> <given-names>A.</given-names></name> <name><surname>Zhao</surname> <given-names>M.</given-names></name> <name><surname>Leavitt</surname> <given-names>J. M.</given-names></name> <name><surname>Lloyd</surname> <given-names>A. M.</given-names></name></person-group> (<year>2008</year>). <article-title>Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings.</article-title> <source><italic>Plant J.</italic></source> <volume>53</volume> <fpage>814</fpage>&#x2013;<lpage>827</lpage>. <pub-id pub-id-type="doi">10.1111/j.1365-313X.2007.03373.x</pub-id> <pub-id pub-id-type="pmid">18036197</pub-id></citation></ref>
<ref id="B70"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gonzali</surname> <given-names>S.</given-names></name> <name><surname>Mazzucato</surname> <given-names>A.</given-names></name> <name><surname>Perata</surname> <given-names>P.</given-names></name></person-group> (<year>2009</year>). <article-title>Purple as a tomato: towards high anthocyanin tomatoes.</article-title> <source><italic>Trends Plant Sci.</italic></source> <volume>14</volume> <fpage>237</fpage>&#x2013;<lpage>241</lpage>. <pub-id pub-id-type="doi">10.1016/j.tplants.2009.02.001</pub-id> <pub-id pub-id-type="pmid">19359211</pub-id></citation></ref>
<ref id="B71"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gudkov</surname> <given-names>S. V.</given-names></name> <name><surname>Grinberg</surname> <given-names>M. A.</given-names></name> <name><surname>Sukhov</surname> <given-names>V.</given-names></name> <name><surname>Vodeneev</surname> <given-names>V.</given-names></name></person-group> (<year>2019</year>). <article-title>Effect of ionizing radiation on physiological and molecular processes in plants.</article-title> <source><italic>J. Environ. Radioact.</italic></source> <volume>202</volume> <fpage>8</fpage>&#x2013;<lpage>24</lpage>. <pub-id pub-id-type="doi">10.1016/j.jenvrad.2019.02.001</pub-id> <pub-id pub-id-type="pmid">30772632</pub-id></citation></ref>
<ref id="B72"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gupta</surname> <given-names>S.</given-names></name> <name><surname>Shi</surname> <given-names>X.</given-names></name> <name><surname>Lindquist</surname> <given-names>I. E.</given-names></name> <name><surname>Devitt</surname> <given-names>N.</given-names></name> <name><surname>Mudge</surname> <given-names>J.</given-names></name> <name><surname>Rashotte</surname> <given-names>A. M.</given-names></name></person-group> (<year>2013</year>). <article-title>Transcriptome profiling of cytokinin and auxin regulation in tomato root.</article-title> <source><italic>J. Exp. Bot.</italic></source> <volume>64</volume> <fpage>695</fpage>&#x2013;<lpage>704</lpage>. <pub-id pub-id-type="doi">10.1093/jxb/ers365</pub-id> <pub-id pub-id-type="pmid">23307920</pub-id></citation></ref>
<ref id="B73"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gutierrez-Valdes</surname> <given-names>N.</given-names></name> <name><surname>H&#x00E4;kkinen</surname> <given-names>S. T.</given-names></name> <name><surname>Lemasson</surname> <given-names>C.</given-names></name> <name><surname>Guillet</surname> <given-names>M.</given-names></name> <name><surname>Oksman-Caldentey</surname> <given-names>K. M.</given-names></name> <name><surname>Ritala</surname> <given-names>A.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Hairy Root Cultures&#x2014;A Versatile Tool With Multiple Applications.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>11</volume>:<issue>33</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2020.00033</pub-id> <pub-id pub-id-type="pmid">32194578</pub-id></citation></ref>
<ref id="B74"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>H&#x00E4;kkinen</surname> <given-names>S. T.</given-names></name> <name><surname>Nygren</surname> <given-names>H.</given-names></name> <name><surname>Nohynek</surname> <given-names>L.</given-names></name> <name><surname>Puupponen-Pimi&#x00E4;</surname> <given-names>R.</given-names></name> <name><surname>Heini&#x00F6;</surname> <given-names>R. L.</given-names></name> <name><surname>Maiorova</surname> <given-names>N.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Plant cell cultures as food&#x2014;aspects of sustainability and safety.</article-title> <source><italic>Plant Cell Rep.</italic></source> <volume>39</volume> <fpage>1655</fpage>&#x2013;<lpage>1668</lpage>. <pub-id pub-id-type="doi">10.1007/s00299-020-02592-2</pub-id> <pub-id pub-id-type="pmid">32892290</pub-id></citation></ref>
<ref id="B75"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hanan</surname> <given-names>A.</given-names></name> <name><surname>Basit</surname> <given-names>A.</given-names></name> <name><surname>Nazir</surname> <given-names>T.</given-names></name> <name><surname>Zeeshan Majeed</surname> <given-names>M.</given-names></name> <name><surname>Qiu</surname> <given-names>D.</given-names></name></person-group> (<year>2020</year>). <article-title>Anti-insect activity of a partially purified protein derived from the entomopathogenic fungus Lecanicillium lecanii (Zimmermann) and its putative role in a tomato defense mechanism against green peach aphid.</article-title> <source><italic>J. Inverteb. Pathol.</italic></source> <volume>11</volume>:<issue>574</issue>. <pub-id pub-id-type="doi">10.1016/j.jip.2019.107282</pub-id> <pub-id pub-id-type="pmid">31759949</pub-id></citation></ref>
<ref id="B76"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Harrison</surname> <given-names>K.</given-names></name> <name><surname>Mendoza-Herrera</surname> <given-names>A.</given-names></name> <name><surname>Levy</surname> <given-names>J. G.</given-names></name> <name><surname>Tamborindeguy</surname> <given-names>C.</given-names></name></person-group> (<year>2021</year>). <article-title>Lasting consequences of psyllid (Bactericera cockerelli L.) infestation on tomato defense, gene expression, and growth.</article-title> <source><italic>BMC Plant Biol.</italic></source> <volume>21</volume>:<issue>114</issue>. <pub-id pub-id-type="doi">10.1186/s12870-021-02876-z</pub-id> <pub-id pub-id-type="pmid">33627099</pub-id></citation></ref>
<ref id="B77"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hawkins</surname> <given-names>C. L.</given-names></name> <name><surname>Davies</surname> <given-names>M. J.</given-names></name></person-group> (<year>2014</year>). <article-title>Detection and characterisation of radicals in biological materials using EPR methodology.</article-title> <source><italic>Biochim. Biophys. Acta</italic></source> <volume>1840</volume> <fpage>708</fpage>&#x2013;<lpage>721</lpage>. <pub-id pub-id-type="doi">10.1016/j.bbagen.2013.03.034</pub-id> <pub-id pub-id-type="pmid">23567797</pub-id></citation></ref>
<ref id="B78"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hilaire</surname> <given-names>M. R.</given-names></name> <name><surname>Ahmed</surname> <given-names>I. A.</given-names></name> <name><surname>Lin</surname> <given-names>C. W.</given-names></name> <name><surname>Jo</surname> <given-names>H.</given-names></name> <name><surname>DeGrado</surname> <given-names>W. F.</given-names></name> <name><surname>Gai</surname> <given-names>F.</given-names></name></person-group> (<year>2017</year>). <article-title>Blue fluorescent amino acid for biological spectroscopy and microscopy.</article-title> <source><italic>Proc. Natl. Acad. Sci. U. S. A.</italic></source> <volume>114</volume> <fpage>6005</fpage>&#x2013;<lpage>6009</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.1705586114</pub-id> <pub-id pub-id-type="pmid">28533371</pub-id></citation></ref>
<ref id="B79"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hoang</surname> <given-names>M. H. T.</given-names></name> <name><surname>Nguyen</surname> <given-names>X. C.</given-names></name> <name><surname>Lee</surname> <given-names>K.</given-names></name> <name><surname>Kwon</surname> <given-names>Y. S.</given-names></name> <name><surname>Pham</surname> <given-names>H. T. T.</given-names></name> <name><surname>Park</surname> <given-names>H. C.</given-names></name><etal/></person-group> (<year>2012</year>). <article-title>Phosphorylation by AtMPK6 is required for the biological function of AtMYB41 in Arabidopsis.</article-title> <source><italic>Biochem. Biophys. Res. Commun.</italic></source> <volume>422</volume> <fpage>181</fpage>&#x2013;<lpage>186</lpage>. <pub-id pub-id-type="doi">10.1016/j.bbrc.2012.04.137</pub-id> <pub-id pub-id-type="pmid">22575450</pub-id></citation></ref>
<ref id="B80"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hou</surname> <given-names>X. J.</given-names></name> <name><surname>Li</surname> <given-names>J. M.</given-names></name> <name><surname>Liu</surname> <given-names>B. L.</given-names></name> <name><surname>Wei</surname> <given-names>L.</given-names></name></person-group> (<year>2017</year>). <article-title>Co-expression of basic helix&#x2013;loop&#x2013;helix protein (bHLH) and transcriptional activator-Myb genes induced anthocyanin biosynthesis in hairy root culture of Nicotiana tabacum L and Ipomea tricolor.</article-title> <source><italic>Acta Physiol. Plantar.</italic></source> <volume>39</volume> <fpage>1</fpage>&#x2013;<lpage>7</lpage>. <pub-id pub-id-type="doi">10.1007/s11738-017-2362-4</pub-id></citation></ref>
<ref id="B81"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hu</surname> <given-names>C.</given-names></name> <name><surname>Gong</surname> <given-names>Y.</given-names></name> <name><surname>Jin</surname> <given-names>S.</given-names></name> <name><surname>Zhu</surname> <given-names>Q.</given-names></name></person-group> (<year>2011</year>). <article-title>Molecular analysis of a UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) gene from purple potato (Solanum tuberosum).</article-title> <source><italic>Mol. Biol. Rep.</italic></source> <volume>38</volume> <fpage>561</fpage>&#x2013;<lpage>567</lpage>. <pub-id pub-id-type="doi">10.1007/s11033-010-0141-z</pub-id> <pub-id pub-id-type="pmid">20358295</pub-id></citation></ref>
<ref id="B82"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname> <given-names>B.</given-names></name> <name><surname>Routaboul</surname> <given-names>J. M.</given-names></name> <name><surname>Liu</surname> <given-names>M.</given-names></name> <name><surname>Deng</surname> <given-names>W.</given-names></name> <name><surname>Maza</surname> <given-names>E.</given-names></name> <name><surname>Mila</surname> <given-names>I.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits.</article-title> <source><italic>J. Exp. Bot.</italic></source> <volume>68</volume> <fpage>4869</fpage>&#x2013;<lpage>4884</lpage>. <pub-id pub-id-type="doi">10.1093/jxb/erx303</pub-id> <pub-id pub-id-type="pmid">28992179</pub-id></citation></ref>
<ref id="B83"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ichikawa</surname> <given-names>H.</given-names></name> <name><surname>Ichiyanagi</surname> <given-names>T.</given-names></name> <name><surname>Xu</surname> <given-names>B.</given-names></name> <name><surname>Yoshii</surname> <given-names>Y.</given-names></name> <name><surname>Nakajima</surname> <given-names>M.</given-names></name> <name><surname>Konishi</surname> <given-names>T.</given-names></name></person-group> (<year>2001</year>). <article-title>Antioxidant activity of anthocyanin extract from purple black rice.</article-title> <source><italic>J. Med. Food</italic></source> <volume>4</volume> <fpage>211</fpage>&#x2013;<lpage>218</lpage>. <pub-id pub-id-type="doi">10.1089/10966200152744481</pub-id> <pub-id pub-id-type="pmid">12639403</pub-id></citation></ref>
<ref id="B84"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Imhof</surname> <given-names>B.</given-names></name> <name><surname>Schlacht</surname> <given-names>I. L.</given-names></name> <name><surname>Waclavicek</surname> <given-names>R.</given-names></name> <name><surname>Schubert</surname> <given-names>D.</given-names></name> <name><surname>Zeidler</surname> <given-names>C.</given-names></name> <name><surname>Vrakking</surname> <given-names>V.</given-names></name><etal/></person-group> (<year>2018</year>). &#x201C;<article-title>Eden Iss &#x2013; A Simulation Testbed To An Advanced Exploration Design Concept For A Greenhouse For Moon And Mars</article-title>&#x201D; in <source><italic>69th International Astronautical Congress.</italic></source> <publisher-loc>Germany</publisher-loc>: <publisher-name>Institute of Space Systems</publisher-name>. <fpage>1</fpage>&#x2013;<lpage>5</lpage>.</citation></ref>
<ref id="B85"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Inglett</surname> <given-names>G. E.</given-names></name> <name><surname>Rose</surname> <given-names>D. J.</given-names></name> <name><surname>Chen</surname> <given-names>D.</given-names></name> <name><surname>Stevenson</surname> <given-names>D. G.</given-names></name> <name><surname>Biswas</surname> <given-names>A.</given-names></name></person-group> (<year>2010</year>). <article-title>Phenolic content and antioxidant activity of extracts from whole buckwheat (Fagopyrum esculentum M&#x00F6;ench) with or without microwave irradiation.</article-title> <source><italic>Food Chem.</italic></source> <volume>119</volume> <fpage>1216</fpage>&#x2013;<lpage>1219</lpage>. <pub-id pub-id-type="doi">10.1016/j.foodchem.2009.07.041</pub-id></citation></ref>
<ref id="B86"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Isaacson</surname> <given-names>T.</given-names></name> <name><surname>Ronen</surname> <given-names>G.</given-names></name> <name><surname>Zamir</surname> <given-names>D.</given-names></name> <name><surname>Hirschberg</surname> <given-names>J.</given-names></name></person-group> (<year>2002</year>). <article-title>Cloning of tangerine from tomato reveals a Carotenoid isomerase essential for the production of &#x03B2;-carotene and xanthophylls in plants.</article-title> <source><italic>Plant Cell</italic></source> <volume>14</volume> <fpage>333</fpage>&#x2013;<lpage>342</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.010303</pub-id> <pub-id pub-id-type="pmid">11884678</pub-id></citation></ref>
<ref id="B87"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Islam</surname> <given-names>A.</given-names></name> <name><surname>Mercer</surname> <given-names>C. F.</given-names></name> <name><surname>Leung</surname> <given-names>S.</given-names></name> <name><surname>Dijkwel</surname> <given-names>P. P.</given-names></name> <name><surname>McManus</surname> <given-names>M. T.</given-names></name></person-group> (<year>2015</year>). <article-title>Transcription of biotic stress associated genes in white clover (Trifolium repens L.) differs in response to cyst and root-knot nematode infection.</article-title> <source><italic>PLoS One</italic></source> <volume>10</volume>:<issue>e0137981</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0137981</pub-id> <pub-id pub-id-type="pmid">26393362</pub-id></citation></ref>
<ref id="B88"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jian</surname> <given-names>W.</given-names></name> <name><surname>Cao</surname> <given-names>H.</given-names></name> <name><surname>Yuan</surname> <given-names>S.</given-names></name> <name><surname>Liu</surname> <given-names>Y.</given-names></name> <name><surname>Lu</surname> <given-names>J.</given-names></name> <name><surname>Lu</surname> <given-names>W.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>SlMYB75, an MYB-type transcription factor, promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits.</article-title> <source><italic>Hortic. Res.</italic></source> <volume>6</volume>:<issue>22</issue>. <pub-id pub-id-type="doi">10.1038/s41438-018-0098-y</pub-id> <pub-id pub-id-type="pmid">30729012</pub-id></citation></ref>
<ref id="B89"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kalt</surname> <given-names>W.</given-names></name> <name><surname>Cassidy</surname> <given-names>A.</given-names></name> <name><surname>Howard</surname> <given-names>L. R.</given-names></name> <name><surname>Krikorian</surname> <given-names>R.</given-names></name> <name><surname>Stull</surname> <given-names>A. J.</given-names></name> <name><surname>Tremblay</surname> <given-names>F.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Recent Research on the Health Benefits of Blueberries and Their Anthocyanins.</article-title> <source><italic>Adv. Nutr.</italic></source> <volume>11</volume> <fpage>224</fpage>&#x2013;<lpage>236</lpage>. <pub-id pub-id-type="doi">10.1093/advances/nmz065</pub-id> <pub-id pub-id-type="pmid">31329250</pub-id></citation></ref>
<ref id="B90"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kashyap</surname> <given-names>S. P.</given-names></name> <name><surname>Prasanna</surname> <given-names>H. C.</given-names></name> <name><surname>Kumari</surname> <given-names>N.</given-names></name> <name><surname>Mishra</surname> <given-names>P.</given-names></name> <name><surname>Singh</surname> <given-names>B.</given-names></name></person-group> (<year>2020</year>). <article-title>Understanding salt tolerance mechanism using transcriptome profiling and de novo assembly of wild tomato Solanum chilense.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>10</volume> <fpage>1</fpage>&#x2013;<lpage>20</lpage>. <pub-id pub-id-type="doi">10.1038/s41598-020-72474-w</pub-id> <pub-id pub-id-type="pmid">32985535</pub-id></citation></ref>
<ref id="B91"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Khandelwal</surname> <given-names>N.</given-names></name> <name><surname>Abraham</surname> <given-names>S. K.</given-names></name></person-group> (<year>2014</year>). <article-title>Intake of anthocyanidins pelargonidin and cyanidin reduces genotoxic stress in mice induced by diepoxybutane, urethane and endogenous nitrosation.</article-title> <source><italic>Environ. Toxicol. Pharmacol.</italic></source> <volume>37</volume> <fpage>837</fpage>&#x2013;<lpage>843</lpage>. <pub-id pub-id-type="doi">10.1016/j.etap.2014.02.012</pub-id> <pub-id pub-id-type="pmid">24642102</pub-id></citation></ref>
<ref id="B92"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Khodadad</surname> <given-names>C. L. M.</given-names></name> <name><surname>Hummerick</surname> <given-names>M. E.</given-names></name> <name><surname>Spencer</surname> <given-names>L. S. E.</given-names></name> <name><surname>Dixit</surname> <given-names>A. R.</given-names></name> <name><surname>Richards</surname> <given-names>J. T.</given-names></name> <name><surname>Romeyn</surname> <given-names>M. W.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Microbiological and Nutritional Analysis of Lettuce Crops Grown on the International Space Station.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>11</volume>:<issue>492</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2020.00199</pub-id> <pub-id pub-id-type="pmid">32210992</pub-id></citation></ref>
<ref id="B93"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kiferle</surname> <given-names>C.</given-names></name> <name><surname>Fantini</surname> <given-names>E.</given-names></name> <name><surname>Bassolino</surname> <given-names>L.</given-names></name> <name><surname>Povero</surname> <given-names>G.</given-names></name> <name><surname>Spelt</surname> <given-names>C.</given-names></name> <name><surname>Buti</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Tomato R2R3-MYB proteins SlANT1 and SlAN2: same protein activity, different roles.</article-title> <source><italic>PLoS One</italic></source> <volume>10</volume>:<issue>e0136365</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0136365</pub-id> <pub-id pub-id-type="pmid">26308527</pub-id></citation></ref>
<ref id="B94"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname> <given-names>D.</given-names></name> <name><surname>Langmead</surname> <given-names>B.</given-names></name> <name><surname>Salzberg</surname> <given-names>S. L.</given-names></name></person-group> (<year>2015</year>). <article-title>HISAT: a fast spliced aligner with low memory requirements Daehwan HHS Public Access.</article-title> <source><italic>Nat. Methods</italic></source> <volume>12</volume> <fpage>357</fpage>&#x2013;<lpage>360</lpage>. <pub-id pub-id-type="doi">10.1038/nmeth.3317.HISAT</pub-id></citation></ref>
<ref id="B95"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname> <given-names>S.</given-names></name> <name><surname>Park</surname> <given-names>J.</given-names></name> <name><surname>Yeom</surname> <given-names>S. I.</given-names></name> <name><surname>Kim</surname> <given-names>Y. M.</given-names></name> <name><surname>Seo</surname> <given-names>E.</given-names></name> <name><surname>Kim</surname> <given-names>K. T.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication.</article-title> <source><italic>Genome Biol.</italic></source> <volume>18</volume> <fpage>1</fpage>&#x2013;<lpage>11</lpage>. <pub-id pub-id-type="doi">10.1186/s13059-017-1341-9</pub-id> <pub-id pub-id-type="pmid">29089032</pub-id></citation></ref>
<ref id="B96"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Klee</surname> <given-names>H. J.</given-names></name> <name><surname>Tieman</surname> <given-names>D. M.</given-names></name></person-group> (<year>2013</year>). <article-title>Genetic challenges of flavor improvement in tomato.</article-title> <source><italic>Trends Genet.</italic></source> <volume>29</volume> <fpage>257</fpage>&#x2013;<lpage>262</lpage>. <pub-id pub-id-type="doi">10.1016/j.tig.2012.12.003</pub-id> <pub-id pub-id-type="pmid">23332147</pub-id></citation></ref>
<ref id="B97"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Koes</surname> <given-names>R.</given-names></name> <name><surname>Verweij</surname> <given-names>W.</given-names></name> <name><surname>Quattrocchio</surname> <given-names>F.</given-names></name></person-group> (<year>2005</year>). <article-title>Flavonoids: a colorful model for the regulation and evolution of biochemical pathways.</article-title> <source><italic>Trends Plant Sci.</italic></source> <volume>10</volume> <fpage>236</fpage>&#x2013;<lpage>242</lpage>. <pub-id pub-id-type="doi">10.1016/j.tplants.2005.03.002</pub-id> <pub-id pub-id-type="pmid">15882656</pub-id></citation></ref>
<ref id="B98"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kozlowski</surname> <given-names>D.</given-names></name> <name><surname>Marsal</surname> <given-names>P.</given-names></name> <name><surname>Steel</surname> <given-names>M.</given-names></name> <name><surname>Mokrini</surname> <given-names>R.</given-names></name> <name><surname>Duroux</surname> <given-names>J. L.</given-names></name> <name><surname>Lazzaroni</surname> <given-names>R.</given-names></name><etal/></person-group> (<year>2007</year>). <article-title>Theoretical investigation of the formation of a new series of antioxidant depsides from the radiolysis of flavonoid compounds.</article-title> <source><italic>Radiat. Res.</italic></source> <volume>168</volume> <fpage>243</fpage>&#x2013;<lpage>252</lpage>. <pub-id pub-id-type="doi">10.1667/RR0824.1</pub-id> <pub-id pub-id-type="pmid">17638407</pub-id></citation></ref>
<ref id="B99"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Krga</surname> <given-names>I.</given-names></name> <name><surname>Milenkovic</surname> <given-names>D.</given-names></name></person-group> (<year>2019</year>). <article-title>Anthocyanins: from Sources and Bioavailability to Cardiovascular-Health Benefits and Molecular Mechanisms of Action.</article-title> <source><italic>J. Agric. Food Chem.</italic></source> <volume>67</volume> <fpage>1771</fpage>&#x2013;<lpage>1783</lpage>. <pub-id pub-id-type="doi">10.1021/acs.jafc.8b06737</pub-id> <pub-id pub-id-type="pmid">30698008</pub-id></citation></ref>
<ref id="B100"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kumar</surname> <given-names>V.</given-names></name> <name><surname>Irfan</surname> <given-names>M.</given-names></name> <name><surname>Ghosh</surname> <given-names>S.</given-names></name> <name><surname>Chakraborty</surname> <given-names>N.</given-names></name> <name><surname>Chakraborty</surname> <given-names>S.</given-names></name> <name><surname>Datta</surname> <given-names>A.</given-names></name></person-group> (<year>2016</year>). <article-title>Fruit ripening mutants reveal cell metabolism and redox state during ripening.</article-title> <source><italic>Protoplasma</italic></source> <volume>253</volume> <fpage>581</fpage>&#x2013;<lpage>594</lpage>. <pub-id pub-id-type="doi">10.1007/s00709-015-0836-z</pub-id> <pub-id pub-id-type="pmid">26008650</pub-id></citation></ref>
<ref id="B101"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lalande</surname> <given-names>M.</given-names></name> <name><surname>Schwob</surname> <given-names>L.</given-names></name> <name><surname>Vizcaino</surname> <given-names>V.</given-names></name> <name><surname>Chirot</surname> <given-names>F.</given-names></name> <name><surname>Dugourd</surname> <given-names>P.</given-names></name> <name><surname>Schlath&#x00F6;lter</surname> <given-names>T.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Direct Radiation Effects on the Structure and Stability of Collagen and Other Proteins.</article-title> <source><italic>ChemBioChem</italic></source> <volume>20</volume> <fpage>2972</fpage>&#x2013;<lpage>2980</lpage>. <pub-id pub-id-type="doi">10.1002/cbic.201900202</pub-id> <pub-id pub-id-type="pmid">31155819</pub-id></citation></ref>
<ref id="B102"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lateef</surname> <given-names>Z. W. A.</given-names></name> <name><surname>Al-Nimer</surname> <given-names>M. S. M.</given-names></name></person-group> (<year>2009</year>). <article-title>X-Rays Irradiation Produced Dual Effects on the Constituents of Medicinal Plants Extracts.</article-title> <source><italic>J. Biol. Sci.</italic></source> <volume>9</volume> <fpage>872</fpage>&#x2013;<lpage>877</lpage>.</citation></ref>
<ref id="B103"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>D.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Ding</surname> <given-names>X.</given-names></name></person-group> (<year>2010</year>). <article-title>Composition and antioxidative properties of the flavonoid-rich fractions from tartary buckwheat grains.</article-title> <source><italic>Food Sci. Biotechnol.</italic></source> <volume>19</volume> <fpage>711</fpage>&#x2013;<lpage>716</lpage>. <pub-id pub-id-type="doi">10.1007/s10068-010-0100-4</pub-id></citation></ref>
<ref id="B104"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>H.</given-names></name> <name><surname>Deng</surname> <given-names>Z.</given-names></name> <name><surname>Liu</surname> <given-names>R.</given-names></name> <name><surname>Young</surname> <given-names>J. C.</given-names></name> <name><surname>Zhu</surname> <given-names>H.</given-names></name> <name><surname>Loewen</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2011</year>). <article-title>Characterization of Phytochemicals and Antioxidant Activities of a Purple Tomato (Solanum lycopersicum L.).</article-title> <source><italic>J. Agric. Food Chem.</italic></source> <volume>59</volume> <fpage>11803</fpage>&#x2013;<lpage>11811</lpage>. <pub-id pub-id-type="doi">10.1021/jf202364v</pub-id> <pub-id pub-id-type="pmid">21905736</pub-id></citation></ref>
<ref id="B105"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>J.</given-names></name> <name><surname>Han</surname> <given-names>G.</given-names></name> <name><surname>Sun</surname> <given-names>C.</given-names></name> <name><surname>Sui</surname> <given-names>N.</given-names></name></person-group> (<year>2019</year>). <article-title>Research advances of MYB transcription factors in plant stress resistance and breeding.</article-title> <source><italic>Plant Signal. Behav.</italic></source> <volume>14</volume> <fpage>1</fpage>&#x2013;<lpage>9</lpage>. <pub-id pub-id-type="doi">10.1080/15592324.2019.1613131</pub-id> <pub-id pub-id-type="pmid">31084451</pub-id></citation></ref>
<ref id="B106"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>Z.</given-names></name> <name><surname>Vickrey</surname> <given-names>T. L.</given-names></name> <name><surname>McNally</surname> <given-names>M. G.</given-names></name> <name><surname>Sato</surname> <given-names>S. J.</given-names></name> <name><surname>Clemente</surname> <given-names>T. E.</given-names></name> <name><surname>Mower</surname> <given-names>J. P.</given-names></name></person-group> (<year>2019</year>). <article-title>Assessing anthocyanin biosynthesis in solanaceae as a model pathway for secondary metabolism.</article-title> <source><italic>Genes</italic></source> <volume>10</volume>:<issue>559</issue>. <pub-id pub-id-type="doi">10.3390/genes10080559</pub-id> <pub-id pub-id-type="pmid">31349565</pub-id></citation></ref>
<ref id="B107"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>N.</given-names></name> <name><surname>Wang</surname> <given-names>J.</given-names></name> <name><surname>Wang</surname> <given-names>B.</given-names></name> <name><surname>Huang</surname> <given-names>S.</given-names></name> <name><surname>Hu</surname> <given-names>J.</given-names></name> <name><surname>Yang</surname> <given-names>T.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Identification of the Carbohydrate and Organic Acid Metabolism Genes Responsible for Brix in Tomato Fruit by Transcriptome and Metabolome Analysis.</article-title> <source><italic>Front. Genet.</italic></source> <volume>12</volume>:<issue>714942</issue>. <pub-id pub-id-type="doi">10.3389/fgene.2021.714942</pub-id> <pub-id pub-id-type="pmid">34539743</pub-id></citation></ref>
<ref id="B108"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>P.</given-names></name> <name><surname>Chen</surname> <given-names>B.</given-names></name> <name><surname>Zhang</surname> <given-names>G.</given-names></name> <name><surname>Chen</surname> <given-names>L.</given-names></name> <name><surname>Dong</surname> <given-names>Q.</given-names></name> <name><surname>Wen</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Regulation of anthocyanin and proanthocyanidin biosynthesis by Medicago truncatula bHLH transcription factor MtTT8.</article-title> <source><italic>New Phytol.</italic></source> <volume>210</volume> <fpage>905</fpage>&#x2013;<lpage>921</lpage>. <pub-id pub-id-type="doi">10.1111/nph.13816</pub-id> <pub-id pub-id-type="pmid">26725247</pub-id></citation></ref>
<ref id="B109"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>P.</given-names></name> <name><surname>Liu</surname> <given-names>H.</given-names></name> <name><surname>Yang</surname> <given-names>H.</given-names></name> <name><surname>Pu</surname> <given-names>X.</given-names></name> <name><surname>Li</surname> <given-names>C.</given-names></name> <name><surname>Huo</surname> <given-names>H.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Translocation of Drought-Responsive Proteins from the Chloroplasts.</article-title> <source><italic>Cells</italic></source> <volume>9</volume> <fpage>1</fpage>&#x2013;<lpage>17</lpage>. <pub-id pub-id-type="doi">10.3390/cells9010259</pub-id> <pub-id pub-id-type="pmid">31968705</pub-id></citation></ref>
<ref id="B110"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Tieman</surname> <given-names>D.</given-names></name> <name><surname>Liu</surname> <given-names>Z.</given-names></name> <name><surname>Chen</surname> <given-names>K.</given-names></name> <name><surname>Klee</surname> <given-names>H. J.</given-names></name></person-group> (<year>2020</year>). <article-title>Identification of a lipase gene with a role in tomato fruit short-chain fatty acid-derived flavor volatiles by genome-wide association.</article-title> <source><italic>Plant J.</italic></source> <volume>104</volume> <fpage>631</fpage>&#x2013;<lpage>644</lpage>. <pub-id pub-id-type="doi">10.1111/tpj.14951</pub-id> <pub-id pub-id-type="pmid">32786123</pub-id></citation></ref>
<ref id="B111"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liao</surname> <given-names>Y.</given-names></name> <name><surname>Smyth</surname> <given-names>G. K.</given-names></name> <name><surname>Shi</surname> <given-names>W.</given-names></name></person-group> (<year>2019</year>). <article-title>The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>47</volume>:<issue>e47</issue>. <pub-id pub-id-type="doi">10.1093/nar/gkz114</pub-id> <pub-id pub-id-type="pmid">30783653</pub-id></citation></ref>
<ref id="B112"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>H.</given-names></name> <name><surname>Liu</surname> <given-names>J.</given-names></name> <name><surname>Wei</surname> <given-names>Y.</given-names></name></person-group> (<year>2016</year>). <article-title>Identification and analysis of the metacaspase gene family in tomato.</article-title> <source><italic>Biochem. Biophys. Res. Commun.</italic></source> <volume>479</volume> <fpage>523</fpage>&#x2013;<lpage>529</lpage>. <pub-id pub-id-type="doi">10.1016/j.bbrc.2016.09.103</pub-id> <pub-id pub-id-type="pmid">27664707</pub-id></citation></ref>
<ref id="B113"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>J.</given-names></name> <name><surname>Osbourn</surname> <given-names>A.</given-names></name> <name><surname>Ma</surname> <given-names>P.</given-names></name></person-group> (<year>2015</year>). <article-title>MYB transcription factors as regulators of phenylpropanoid metabolism in plants.</article-title> <source><italic>Mol. Plant</italic></source> <volume>8</volume> <fpage>689</fpage>&#x2013;<lpage>708</lpage>. <pub-id pub-id-type="doi">10.1016/j.molp.2015.03.012</pub-id> <pub-id pub-id-type="pmid">25840349</pub-id></citation></ref>
<ref id="B114"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>Y.</given-names></name> <name><surname>Tikunov</surname> <given-names>Y.</given-names></name> <name><surname>Schouten</surname> <given-names>R. E.</given-names></name> <name><surname>Marcelis</surname> <given-names>L. F. M.</given-names></name> <name><surname>Visser</surname> <given-names>R. G. F.</given-names></name> <name><surname>Bovy</surname> <given-names>A.</given-names></name></person-group> (<year>2018</year>). <article-title>Anthocyanin biosynthesis and degradation mechanisms in Solanaceous vegetables: a review.</article-title> <source><italic>Front. Chem.</italic></source> <volume>6</volume>:<issue>52</issue>. <pub-id pub-id-type="doi">10.3389/fchem.2018.00052</pub-id> <pub-id pub-id-type="pmid">29594099</pub-id></citation></ref>
<ref id="B115"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Livak</surname> <given-names>K. J.</given-names></name> <name><surname>Schmittgen</surname> <given-names>T. D.</given-names></name></person-group> (<year>2001</year>). <article-title>Analysis of relative gene expression data using real-time quantitative PCR and the 2-&#x0394;&#x0394;CT method.</article-title> <source><italic>Methods</italic></source> <volume>25</volume> <fpage>402</fpage>&#x2013;<lpage>408</lpage>. <pub-id pub-id-type="doi">10.1006/meth.2001.1262</pub-id> <pub-id pub-id-type="pmid">11846609</pub-id></citation></ref>
<ref id="B116"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lloyd</surname> <given-names>A.</given-names></name> <name><surname>Brockman</surname> <given-names>A.</given-names></name> <name><surname>Aguirre</surname> <given-names>L.</given-names></name> <name><surname>Campbell</surname> <given-names>A.</given-names></name> <name><surname>Bean</surname> <given-names>A.</given-names></name> <name><surname>Cantero</surname> <given-names>A.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Advances in the MYB-bHLH-WD Repeat (MBW) pigment regulatory model: addition of a WRKY factor and co-option of an anthocyanin MYB for betalain regulation.</article-title> <source><italic>Plant Cell Physiol</italic></source> <volume>58</volume> <fpage>1431</fpage>&#x2013;<lpage>1441</lpage>. <pub-id pub-id-type="doi">10.1093/pcp/pcx075</pub-id> <pub-id pub-id-type="pmid">28575507</pub-id></citation></ref>
<ref id="B117"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lohmann</surname> <given-names>W.</given-names></name> <name><surname>Lohmann</surname> <given-names>C.</given-names></name> <name><surname>Ibrahim</surname> <given-names>M.</given-names></name></person-group> (<year>1988</year>). <article-title>Fluorescence spectra of NADH/NAD, kynurenine, tryptophan, and tyrosine.</article-title> <source><italic>Naturwissenschaften</italic></source> <volume>75</volume> <fpage>141</fpage>&#x2013;<lpage>142</lpage>. <pub-id pub-id-type="doi">10.1007/BF00405305</pub-id> <pub-id pub-id-type="pmid">3380163</pub-id></citation></ref>
<ref id="B118"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lotito</surname> <given-names>S. B.</given-names></name> <name><surname>Frei</surname> <given-names>B.</given-names></name></person-group> (<year>2006</year>). <article-title>Consumption of flavonoid-rich foods and increased plasma antioxidant capacity in humans: cause, consequence, or epiphenomenon?</article-title> <source><italic>Free Radic. Biol. Med.</italic></source> <volume>41</volume> <fpage>1727</fpage>&#x2013;<lpage>1746</lpage>. <pub-id pub-id-type="doi">10.1016/j.freeradbiomed.2006.04.033</pub-id> <pub-id pub-id-type="pmid">17157175</pub-id></citation></ref>
<ref id="B119"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Love</surname> <given-names>M. I.</given-names></name> <name><surname>Huber</surname> <given-names>W.</given-names></name> <name><surname>Anders</surname> <given-names>S.</given-names></name></person-group> (<year>2014</year>). <article-title>Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.</article-title> <source><italic>Genome Biol.</italic></source> <volume>15</volume> <fpage>1</fpage>&#x2013;<lpage>21</lpage>. <pub-id pub-id-type="doi">10.1186/s13059-014-0550-8</pub-id> <pub-id pub-id-type="pmid">25516281</pub-id></citation></ref>
<ref id="B120"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Marcu</surname> <given-names>D.</given-names></name> <name><surname>Cristea</surname> <given-names>V.</given-names></name> <name><surname>Daraban</surname> <given-names>L.</given-names></name></person-group> (<year>2013a</year>). <article-title>Dose-dependent effects of gamma radiation on lettuce (Lactuca sativa var. capitata) seedlings.</article-title> <source><italic>Int. J. Radiat. Biol.</italic></source> <volume>89</volume> <fpage>219</fpage>&#x2013;<lpage>223</lpage>. <pub-id pub-id-type="doi">10.3109/09553002.2013.734946</pub-id> <pub-id pub-id-type="pmid">23020834</pub-id></citation></ref>
<ref id="B121"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Marcu</surname> <given-names>D.</given-names></name> <name><surname>Damian</surname> <given-names>G.</given-names></name> <name><surname>Cosma</surname> <given-names>C.</given-names></name></person-group> (<year>2013b</year>). <article-title>Gamma radiation effects on seed germination, growth and pigment content, and ESR study of induced free radicals in maize (Zea mays).</article-title> <source><italic>J. Biol. Phys.</italic></source> <volume>39</volume> <fpage>625</fpage>&#x2013;<lpage>634</lpage>. <pub-id pub-id-type="doi">10.1007/s10867-013-9322-z</pub-id> <pub-id pub-id-type="pmid">23996407</pub-id></citation></ref>
<ref id="B122"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Meng</surname> <given-names>X.</given-names></name> <name><surname>Yang</surname> <given-names>D.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Zhao</surname> <given-names>S.</given-names></name> <name><surname>Sui</surname> <given-names>N.</given-names></name> <name><surname>Meng</surname> <given-names>Q.</given-names></name></person-group> (<year>2015</year>). <article-title>Physiological changes in fruit ripening caused by overexpression of tomato SlAN2, an R2R3-MYB factor.</article-title> <source><italic>Plant Physiol. Biochem.</italic></source> <volume>89</volume> <fpage>24</fpage>&#x2013;<lpage>30</lpage>. <pub-id pub-id-type="doi">10.1016/j.plaphy.2015.02.005</pub-id> <pub-id pub-id-type="pmid">25698665</pub-id></citation></ref>
<ref id="B123"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mart&#x00ED;</surname> <given-names>R.</given-names></name> <name><surname>Rosell&#x00F3;</surname> <given-names>S.</given-names></name> <name><surname>Cebolla-Cornejo</surname> <given-names>J.</given-names></name></person-group> (<year>2016</year>). <article-title>Tomato as a source of carotenoids and polyphenols targeted to cancer prevention.</article-title> <source><italic>Cancers</italic></source> <volume>8</volume> <fpage>1</fpage>&#x2013;<lpage>28</lpage>. <pub-id pub-id-type="doi">10.3390/cancers8060058</pub-id> <pub-id pub-id-type="pmid">27331820</pub-id></citation></ref>
<ref id="B124"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Massa</surname> <given-names>G. D.</given-names></name> <name><surname>Wheeler</surname> <given-names>R. M.</given-names></name> <name><surname>Morrow</surname> <given-names>R. C.</given-names></name> <name><surname>Levine</surname> <given-names>H. G.</given-names></name></person-group> (<year>2016</year>). <article-title>Growth chambers on the International Space Station for large plants.</article-title> <source><italic>Acta Hortic.</italic></source> <volume>1134</volume> <fpage>215</fpage>&#x2013;<lpage>221</lpage>. <pub-id pub-id-type="doi">10.17660/ActaHortic.2016.1134.29</pub-id> <pub-id pub-id-type="pmid">34854763</pub-id></citation></ref>
<ref id="B125"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mathews</surname> <given-names>H.</given-names></name> <name><surname>Clendennen</surname> <given-names>S. K.</given-names></name> <name><surname>Caldwell</surname> <given-names>C. G.</given-names></name> <name><surname>Liu</surname> <given-names>X. L.</given-names></name> <name><surname>Connors</surname> <given-names>K.</given-names></name> <name><surname>Matheis</surname> <given-names>N.</given-names></name><etal/></person-group> (<year>2003</year>). <article-title>Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport.</article-title> <source><italic>Plant Cell</italic></source> <volume>15</volume> <fpage>1689</fpage>&#x2013;<lpage>1703</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.012963</pub-id> <pub-id pub-id-type="pmid">12897245</pub-id></citation></ref>
<ref id="B126"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mazzucato</surname> <given-names>A.</given-names></name> <name><surname>Willems</surname> <given-names>D.</given-names></name> <name><surname>Bernini</surname> <given-names>R.</given-names></name> <name><surname>Picarella</surname> <given-names>M. E.</given-names></name> <name><surname>Santangelo</surname> <given-names>E.</given-names></name> <name><surname>Ruiu</surname> <given-names>F.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>Novel phenotypes related to the breeding of purple-fruited tomatoes and effect of peel extracts on human cancer cell proliferation.</article-title> <source><italic>Plant Physiol. Biochem.</italic></source> <volume>72</volume> <fpage>125</fpage>&#x2013;<lpage>133</lpage>. <pub-id pub-id-type="doi">10.1016/J.PLAPHY.2013.05.012</pub-id> <pub-id pub-id-type="pmid">23769702</pub-id></citation></ref>
<ref id="B127"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>McLellan</surname> <given-names>H.</given-names></name> <name><surname>Gilroy</surname> <given-names>E. M.</given-names></name> <name><surname>Yun</surname> <given-names>B. W.</given-names></name> <name><surname>Birch</surname> <given-names>P. R. J.</given-names></name> <name><surname>Loake</surname> <given-names>G. J.</given-names></name></person-group> (<year>2009</year>). <article-title>Functional redundancy in the Arabidopsis Cathepsin B gene family contributes to basal defence, the hypersensitive response and senescence.</article-title> <source><italic>New Phytol.</italic></source> <volume>183</volume> <fpage>408</fpage>&#x2013;<lpage>418</lpage>. <pub-id pub-id-type="doi">10.1111/j.1469-8137.2009.02865.x</pub-id> <pub-id pub-id-type="pmid">19453434</pub-id></citation></ref>
<ref id="B128"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mehrtens</surname> <given-names>F.</given-names></name> <name><surname>Kranz</surname> <given-names>H.</given-names></name> <name><surname>Bednarek</surname> <given-names>P.</given-names></name> <name><surname>Weisshaar</surname> <given-names>B.</given-names></name></person-group> (<year>2005</year>). <article-title>The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>138</volume> <fpage>1083</fpage>&#x2013;<lpage>1096</lpage>. <pub-id pub-id-type="doi">10.1104/pp.104.058032</pub-id> <pub-id pub-id-type="pmid">15923334</pub-id></citation></ref>
<ref id="B129"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mei</surname> <given-names>W.</given-names></name> <name><surname>Qin</surname> <given-names>Y.</given-names></name> <name><surname>Song</surname> <given-names>W.</given-names></name> <name><surname>Li</surname> <given-names>J.</given-names></name> <name><surname>Zhu</surname> <given-names>Y.</given-names></name></person-group> (<year>2009</year>). <article-title>Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation.</article-title> <source><italic>J. Genet. Genomics</italic></source> <volume>36</volume> <fpage>141</fpage>&#x2013;<lpage>150</lpage>. <pub-id pub-id-type="doi">10.1016/S1673-8527(08)60101-0</pub-id></citation></ref>
<ref id="B130"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mes</surname> <given-names>P. J.</given-names></name> <name><surname>Boches</surname> <given-names>P.</given-names></name> <name><surname>Myers</surname> <given-names>J. R.</given-names></name> <name><surname>Durst</surname> <given-names>R.</given-names></name></person-group> (<year>2008</year>). <article-title>Characterization of tomatoes expressing anthocyanin in the fruit.</article-title> <source><italic>J. Am. Soc. Hortic. Sci.</italic></source> <volume>133</volume> <fpage>262</fpage>&#x2013;<lpage>269</lpage>. <pub-id pub-id-type="doi">10.21273/jashs.133.2.262</pub-id></citation></ref>
<ref id="B131"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mikami</surname> <given-names>K.</given-names></name> <name><surname>Hosokawa</surname> <given-names>M.</given-names></name></person-group> (<year>2013</year>). <article-title>Biosynthetic pathway and health benefits of fucoxanthin, an algae-specific xanthophyll in brown seaweeds.</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>14</volume> <fpage>13763</fpage>&#x2013;<lpage>13781</lpage>. <pub-id pub-id-type="doi">10.3390/ijms140713763</pub-id> <pub-id pub-id-type="pmid">23820585</pub-id></citation></ref>
<ref id="B132"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Moghaddam</surname> <given-names>S. S.</given-names></name> <name><surname>Jaafar</surname> <given-names>H.</given-names></name> <name><surname>Ibrahim</surname> <given-names>R.</given-names></name> <name><surname>Rahmat</surname> <given-names>A.</given-names></name> <name><surname>Aziz</surname> <given-names>M. A.</given-names></name> <name><surname>Philip</surname> <given-names>E.</given-names></name></person-group> (<year>2011</year>). <article-title>Effects of acute gamma irradiation on physiological traits and flavonoid accumulation of <italic>Centella asiatica</italic>.</article-title> <source><italic>Molecules</italic></source> <volume>16</volume> <fpage>4994</fpage>&#x2013;<lpage>5007</lpage>. <pub-id pub-id-type="doi">10.3390/molecules16064994</pub-id> <pub-id pub-id-type="pmid">21694666</pub-id></citation></ref>
<ref id="B133"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Morishita</surname> <given-names>T.</given-names></name> <name><surname>Yamaguchi</surname> <given-names>H.</given-names></name> <name><surname>Degi</surname> <given-names>K.</given-names></name></person-group> (<year>2007</year>). <article-title>The contribution of polyphenols to antioxidative activity in common buckwheat and Tartary buckwheat grain.</article-title> <source><italic>Plant Prod. Sci.</italic></source> <volume>10</volume> <fpage>99</fpage>&#x2013;<lpage>104</lpage>. <pub-id pub-id-type="doi">10.1626/pps.10.99</pub-id> <pub-id pub-id-type="pmid">34921734</pub-id></citation></ref>
<ref id="B134"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Morita</surname> <given-names>Y.</given-names></name> <name><surname>Takagi</surname> <given-names>K.</given-names></name> <name><surname>Fukuchi-Mizutani</surname> <given-names>M.</given-names></name> <name><surname>Ishiguro</surname> <given-names>K.</given-names></name> <name><surname>Tanaka</surname> <given-names>Y.</given-names></name> <name><surname>Nitasaka</surname> <given-names>E.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>A chalcone isomerase-like protein enhances flavonoid production and flower pigmentation.</article-title> <source><italic>Plant J.</italic></source> <volume>78</volume> <fpage>294</fpage>&#x2013;<lpage>304</lpage>. <pub-id pub-id-type="doi">10.1111/tpj.12469</pub-id> <pub-id pub-id-type="pmid">24517863</pub-id></citation></ref>
<ref id="B135"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Murata</surname> <given-names>M.</given-names></name> <name><surname>Nakai</surname> <given-names>Y.</given-names></name> <name><surname>Kawazu</surname> <given-names>K.</given-names></name> <name><surname>Ishizaka</surname> <given-names>M.</given-names></name> <name><surname>Kajiwara</surname> <given-names>H.</given-names></name> <name><surname>Ab</surname> <given-names>H.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Loliolide, a carotenoid metabolite, is a potential endogenous inducer of herbivore resistance.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>179</volume> <fpage>1822</fpage>&#x2013;<lpage>1833</lpage>. <pub-id pub-id-type="doi">10.1104/pp.18.00837</pub-id> <pub-id pub-id-type="pmid">30700538</pub-id></citation></ref>
<ref id="B136"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Nagata</surname> <given-names>T.</given-names></name> <name><surname>Todoriki</surname> <given-names>S.</given-names></name> <name><surname>Masumizu</surname> <given-names>T.</given-names></name> <name><surname>Suda</surname> <given-names>I.</given-names></name> <name><surname>Furuta</surname> <given-names>S.</given-names></name> <name><surname>Du</surname> <given-names>Z.</given-names></name><etal/></person-group> (<year>2003</year>). <article-title>Levels of active oxygen species are controlled by ascorbic acid and anthocyanin in Arabidopsis.</article-title> <source><italic>J. Agric. Food Chem.</italic></source> <volume>51</volume> <fpage>2992</fpage>&#x2013;<lpage>2999</lpage>. <pub-id pub-id-type="doi">10.1021/jf026179+</pub-id> <pub-id pub-id-type="pmid">12720382</pub-id></citation></ref>
<ref id="B137"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Nveawiah-Yoho</surname> <given-names>P.</given-names></name> <name><surname>Zhou</surname> <given-names>J.</given-names></name> <name><surname>Palmer</surname> <given-names>M.</given-names></name> <name><surname>Sauve</surname> <given-names>R.</given-names></name> <name><surname>Zhou</surname> <given-names>S.</given-names></name> <name><surname>Howe</surname> <given-names>K. J.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>Identification of Proteins for Salt Tolerance Using a Comparative Proteomics Analysis of Tomato Accessions with Contrasting Salt Tolerance.</article-title> <source><italic>J. Am. Soc. Hortic. Sci.</italic></source> <volume>138</volume>:<issue>13</issue>. <pub-id pub-id-type="doi">10.21273/jashs.138.5.382</pub-id></citation></ref>
<ref id="B138"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Omidvar</surname> <given-names>V.</given-names></name> <name><surname>Mohorianu</surname> <given-names>I.</given-names></name> <name><surname>Dalmay</surname> <given-names>T.</given-names></name> <name><surname>Fellner</surname> <given-names>M.</given-names></name></person-group> (<year>2015</year>). <article-title>Identification of miRNAs with potential roles in regulation of anther development and male-sterility in 7B-1 male-sterile tomato mutant.</article-title> <source><italic>BMC Genomics</italic></source> <volume>16</volume>:<issue>878</issue>. <pub-id pub-id-type="doi">10.1186/s12864-015-2077-0</pub-id> <pub-id pub-id-type="pmid">26511108</pub-id></citation></ref>
<ref id="B139"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ooe</surname> <given-names>E.</given-names></name> <name><surname>Ogawa</surname> <given-names>K.</given-names></name> <name><surname>Horiuchi</surname> <given-names>T.</given-names></name> <name><surname>Tada</surname> <given-names>H.</given-names></name> <name><surname>Murase</surname> <given-names>H.</given-names></name> <name><surname>Tsuruma</surname> <given-names>K.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Analysis and characterization of anthocyanins and carotenoids in Japanese blue tomato.</article-title> <source><italic>Biosci. Biotechnol. Biochem.</italic></source> <volume>80</volume> <fpage>341</fpage>&#x2013;<lpage>349</lpage>. <pub-id pub-id-type="doi">10.1080/09168451.2015.1091715</pub-id> <pub-id pub-id-type="pmid">26443075</pub-id></citation></ref>
<ref id="B140"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pan</surname> <given-names>Q.</given-names></name> <name><surname>Liu</surname> <given-names>Y. S.</given-names></name> <name><surname>Budai-Hadrian</surname> <given-names>O.</given-names></name> <name><surname>Sela</surname> <given-names>M.</given-names></name> <name><surname>Carmel-Goren</surname> <given-names>L.</given-names></name> <name><surname>Zamir</surname> <given-names>D.</given-names></name><etal/></person-group> (<year>2000</year>). <article-title>Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologues in the genomes of two dicotyledons: tomato and arabidopsis.</article-title> <source><italic>Genetics</italic></source> <volume>155</volume> <fpage>309</fpage>&#x2013;<lpage>322</lpage>. <pub-id pub-id-type="doi">10.1093/genetics/155.1.309</pub-id> <pub-id pub-id-type="pmid">10790405</pub-id></citation></ref>
<ref id="B141"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pan</surname> <given-names>X.</given-names></name> <name><surname>Wang</surname> <given-names>G.</given-names></name> <name><surname>Lay</surname> <given-names>C. L.</given-names></name> <name><surname>Tan</surname> <given-names>B. H.</given-names></name> <name><surname>He</surname> <given-names>C.</given-names></name> <name><surname>Liu</surname> <given-names>Y.</given-names></name></person-group> (<year>2013</year>). <article-title>Photoluminescence from Amino-Containing Polymer in the Presence of CO 2: carbamato Anion Formed as a Fluorophore.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>3</volume> <fpage>1</fpage>&#x2013;<lpage>6</lpage>. <pub-id pub-id-type="doi">10.1038/srep02763</pub-id> <pub-id pub-id-type="pmid">24067377</pub-id></citation></ref>
<ref id="B142"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Paniagua</surname> <given-names>C.</given-names></name> <name><surname>Bilkova</surname> <given-names>A.</given-names></name> <name><surname>Jackson</surname> <given-names>P.</given-names></name> <name><surname>Dabravolski</surname> <given-names>S.</given-names></name> <name><surname>Riber</surname> <given-names>W.</given-names></name> <name><surname>Didi</surname> <given-names>V.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Dirigent proteins in plants: modulating cell wall metabolism during abiotic and biotic stress exposure.</article-title> <source><italic>J. Exp. Bot.</italic></source> <volume>68</volume> <fpage>3287</fpage>&#x2013;<lpage>3301</lpage>. <pub-id pub-id-type="doi">10.1093/jxb/erx141</pub-id> <pub-id pub-id-type="pmid">28472349</pub-id></citation></ref>
<ref id="B143"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pelletier</surname> <given-names>K.</given-names></name> <name><surname>Murrell</surname> <given-names>J. R.</given-names></name> <name><surname>Shirley</surname> <given-names>B. W.</given-names></name></person-group> (<year>1997</year>). <article-title>Characterization of flavonol synthase and leucoanthocyanidin dioxygenase genes in Arabidopsis. Further evidence for differential regulation of &#x201C;early&#x201D; and &#x201C;late&#x201D; genes.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>113</volume> <fpage>1437</fpage>&#x2013;<lpage>1445</lpage>. <pub-id pub-id-type="doi">10.1104/pp.113.4.1437</pub-id> <pub-id pub-id-type="pmid">9112784</pub-id></citation></ref>
<ref id="B144"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Peng</surname> <given-names>H.</given-names></name> <name><surname>Yang</surname> <given-names>T.</given-names></name> <name><surname>Jurick</surname> <given-names>W. M.</given-names></name></person-group> (<year>2014</year>). <article-title>Calmodulin gene expression in response to mechanical wounding and Botrytis cinerea infection in tomato fruit.</article-title> <source><italic>Plants</italic></source> <volume>3</volume> <fpage>427</fpage>&#x2013;<lpage>441</lpage>. <pub-id pub-id-type="doi">10.3390/plants3030427</pub-id> <pub-id pub-id-type="pmid">27135512</pub-id></citation></ref>
<ref id="B145"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Peng</surname> <given-names>J.</given-names></name> <name><surname>Deng</surname> <given-names>X.</given-names></name> <name><surname>Huang</surname> <given-names>J.</given-names></name> <name><surname>Jia</surname> <given-names>S.</given-names></name> <name><surname>Miao</surname> <given-names>X.</given-names></name> <name><surname>Huang</surname> <given-names>Y.</given-names></name></person-group> (<year>2004</year>). <article-title>Role of salicylic acid in tomato defense against cotton bollworm, Helicoverpa armigera Hubner.</article-title> <source><italic>Z. Naturforsch. C J. Biosci.</italic></source> <volume>59</volume> <fpage>856</fpage>&#x2013;<lpage>862</lpage>. <pub-id pub-id-type="doi">10.1515/znc-2004-11-1215</pub-id> <pub-id pub-id-type="pmid">15666546</pub-id></citation></ref>
<ref id="B146"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Petrisor</surname> <given-names>D.</given-names></name> <name><surname>Damian</surname> <given-names>G.</given-names></name> <name><surname>Simon</surname> <given-names>S.</given-names></name> <name><surname>Hosu</surname> <given-names>A.</given-names></name> <name><surname>Miclaus</surname> <given-names>V.</given-names></name></person-group> (<year>2008</year>). <article-title>Antioxidant activity of some types of white wines and juices investigated by EPR spectroscopy.</article-title> <source><italic>Mod. Phys. Lett. B</italic></source> <volume>22</volume> <fpage>2689</fpage>&#x2013;<lpage>2698</lpage>. <pub-id pub-id-type="doi">10.1142/S0217984908017175</pub-id></citation></ref>
<ref id="B147"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pinheiro</surname> <given-names>T. T.</given-names></name> <name><surname>Peres</surname> <given-names>L. E. P.</given-names></name> <name><surname>Purgatto</surname> <given-names>E.</given-names></name> <name><surname>Latado</surname> <given-names>R. R.</given-names></name> <name><surname>Maniero</surname> <given-names>R. A.</given-names></name> <name><surname>Martins</surname> <given-names>M. M.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Citrus carotenoid isomerase gene characterization by complementation of the &#x201C;Micro-Tom&#x201D; tangerine mutant.</article-title> <source><italic>Plant Cell Rep.</italic></source> <volume>38</volume> <fpage>623</fpage>&#x2013;<lpage>636</lpage>. <pub-id pub-id-type="doi">10.1007/s00299-019-02393-2</pub-id> <pub-id pub-id-type="pmid">30737538</pub-id></citation></ref>
<ref id="B148"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Povero</surname> <given-names>G.</given-names></name></person-group> (<year>2011</year>). <source><italic>Physiological and Genetic Control of Anthocyanin Pigmentation in Different Species.</italic></source> <publisher-loc>Netherlands</publisher-loc>: <publisher-name>Vrije Universiteit Amsterdam</publisher-name>.</citation></ref>
<ref id="B149"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Povero</surname> <given-names>G.</given-names></name> <name><surname>Gonzali</surname> <given-names>S.</given-names></name> <name><surname>Bassolino</surname> <given-names>L.</given-names></name> <name><surname>Mazzucato</surname> <given-names>A.</given-names></name> <name><surname>Perata</surname> <given-names>P.</given-names></name></person-group> (<year>2011</year>). <article-title>Transcriptional analysis in high-anthocyanin tomatoes reveals synergistic effect of Aft and atv genes.</article-title> <source><italic>J. Plant Physiol.</italic></source> <volume>168</volume> <fpage>270</fpage>&#x2013;<lpage>279</lpage>. <pub-id pub-id-type="doi">10.1016/j.jplph.2010.07.022</pub-id> <pub-id pub-id-type="pmid">20888667</pub-id></citation></ref>
<ref id="B150"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Preu&#x00DF;</surname> <given-names>A.</given-names></name> <name><surname>Stracke</surname> <given-names>R.</given-names></name> <name><surname>Weisshaar</surname> <given-names>B.</given-names></name> <name><surname>Hillebrecht</surname> <given-names>A.</given-names></name> <name><surname>Matern</surname> <given-names>U.</given-names></name> <name><surname>Martens</surname> <given-names>S.</given-names></name></person-group> (<year>2009</year>). <article-title>Arabidopsis thaliana expresses a second functional flavonol synthase.</article-title> <source><italic>FEBS Lett.</italic></source> <volume>583</volume> <fpage>1981</fpage>&#x2013;<lpage>1986</lpage>. <pub-id pub-id-type="doi">10.1016/j.febslet.2009.05.006</pub-id> <pub-id pub-id-type="pmid">19433090</pub-id></citation></ref>
<ref id="B151"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Qian</surname> <given-names>Y.</given-names></name> <name><surname>Zhang</surname> <given-names>T.</given-names></name> <name><surname>Yu</surname> <given-names>Y.</given-names></name> <name><surname>Gou</surname> <given-names>L.</given-names></name> <name><surname>Yang</surname> <given-names>J.</given-names></name> <name><surname>Xu</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Regulatory Mechanisms of bHLH Transcription Factors in Plant Adaptive Responses to Various Abiotic Stresses.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>12</volume>:<issue>677611</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2021.677611</pub-id> <pub-id pub-id-type="pmid">34220896</pub-id></citation></ref>
<ref id="B152"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Qiu</surname> <given-names>Z.</given-names></name> <name><surname>Wang</surname> <given-names>X.</given-names></name> <name><surname>Gao</surname> <given-names>J.</given-names></name> <name><surname>Guo</surname> <given-names>Y.</given-names></name> <name><surname>Huang</surname> <given-names>Z.</given-names></name> <name><surname>Du</surname> <given-names>Y.</given-names></name></person-group> (<year>2016</year>). <article-title>The Tomato Hoffman&#x2019;s Anthocyaninless Gene Encodes a bHLH Transcription Factor Involved in Anthocyanin Biosynthesis That Is Developmentally Regulated and Induced by Low Temperatures.</article-title> <source><italic>PLoS One</italic></source> <volume>11</volume>:<issue>e0151067</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0151067</pub-id> <pub-id pub-id-type="pmid">26943362</pub-id></citation></ref>
<ref id="B153"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ramsay</surname> <given-names>N. A.</given-names></name> <name><surname>Glover</surname> <given-names>B. J.</given-names></name></person-group> (<year>2005</year>). <article-title>MYB-bHLH-WD40 protein complex and the evolution of cellular diversity.</article-title> <source><italic>Trends Plant Sci.</italic></source> <volume>10</volume> <fpage>63</fpage>&#x2013;<lpage>70</lpage>. <pub-id pub-id-type="doi">10.1016/j.tplants.2004.12.011</pub-id> <pub-id pub-id-type="pmid">15708343</pub-id></citation></ref>
<ref id="B154"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Reimand</surname> <given-names>J.</given-names></name> <name><surname>Kull</surname> <given-names>M.</given-names></name> <name><surname>Peterson</surname> <given-names>H.</given-names></name> <name><surname>Hansen</surname> <given-names>J.</given-names></name> <name><surname>Vilo</surname> <given-names>J.</given-names></name></person-group> (<year>2007</year>). <article-title>G:Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>35</volume> <fpage>193</fpage>&#x2013;<lpage>200</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkm226</pub-id> <pub-id pub-id-type="pmid">17478515</pub-id></citation></ref>
<ref id="B155"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Riley</surname> <given-names>P. A.</given-names></name></person-group> (<year>1994</year>). <article-title>Free Radicals in Biology: oxidative Stress and the Effects of Ionizing Radiation.</article-title> <source><italic>Int. J. Radiat. Biol.</italic></source> <volume>65</volume> <fpage>27</fpage>&#x2013;<lpage>33</lpage>.</citation></ref>
<ref id="B156"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Roldan</surname> <given-names>M. V. G.</given-names></name> <name><surname>Outchkourov</surname> <given-names>N.</given-names></name> <name><surname>van Houwelingen</surname> <given-names>A.</given-names></name> <name><surname>Lammers</surname> <given-names>M.</given-names></name> <name><surname>de La Fuente</surname> <given-names>I. R.</given-names></name> <name><surname>Ziklo</surname> <given-names>N.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>An O-methyltransferase modifies accumulation of methylated anthocyanins in seedlings of tomato.</article-title> <source><italic>Plant J.</italic></source> <volume>80</volume> <fpage>695</fpage>&#x2013;<lpage>708</lpage>. <pub-id pub-id-type="doi">10.1111/tpj.12664</pub-id> <pub-id pub-id-type="pmid">25227758</pub-id></citation></ref>
<ref id="B157"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ron</surname> <given-names>M.</given-names></name> <name><surname>Kajala</surname> <given-names>K.</given-names></name> <name><surname>Pauluzzi</surname> <given-names>G.</given-names></name> <name><surname>Wang</surname> <given-names>D.</given-names></name> <name><surname>Reynoso</surname> <given-names>M. A.</given-names></name> <name><surname>Zumstein</surname> <given-names>K.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>166</volume> <fpage>455</fpage>&#x2013;<lpage>469</lpage>. <pub-id pub-id-type="doi">10.1104/pp.114.239392</pub-id> <pub-id pub-id-type="pmid">24868032</pub-id></citation></ref>
<ref id="B158"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Rossetto</surname> <given-names>M.</given-names></name> <name><surname>Vanzani</surname> <given-names>P.</given-names></name> <name><surname>Lunelli</surname> <given-names>M.</given-names></name> <name><surname>Scarpa</surname> <given-names>M.</given-names></name> <name><surname>Mattivi</surname> <given-names>F.</given-names></name> <name><surname>Rigo</surname> <given-names>A.</given-names></name></person-group> (<year>2007</year>). <article-title>Peroxyl radical trapping activity of anthocyanins and generation of free radical intermediates.</article-title> <source><italic>Free Radic. Res.</italic></source> <volume>41</volume> <fpage>854</fpage>&#x2013;<lpage>859</lpage>. <pub-id pub-id-type="doi">10.1080/10715760701261533</pub-id> <pub-id pub-id-type="pmid">17577747</pub-id></citation></ref>
<ref id="B159"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Roy</surname> <given-names>S.</given-names></name></person-group> (<year>2016</year>). <article-title>Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome.</article-title> <source><italic>Plant Signal. Behav.</italic></source> <volume>11</volume>:<issue>e1117723</issue>. <pub-id pub-id-type="doi">10.1080/15592324.2015.1117723</pub-id> <pub-id pub-id-type="pmid">26636625</pub-id></citation></ref>
<ref id="B160"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Safavi-Rizi</surname> <given-names>V.</given-names></name> <name><surname>Herde</surname> <given-names>M.</given-names></name> <name><surname>St&#x00F6;hr</surname> <given-names>C.</given-names></name></person-group> (<year>2020</year>). <article-title>Identification of nitric oxide (NO)-responsive genes under hypoxia in tomato (Solanum lycopersicum L.) root.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>10</volume> <fpage>1</fpage>&#x2013;<lpage>20</lpage>. <pub-id pub-id-type="doi">10.1038/s41598-020-73613-z</pub-id> <pub-id pub-id-type="pmid">33020554</pub-id></citation></ref>
<ref id="B161"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Saha</surname> <given-names>S.</given-names></name> <name><surname>Singh</surname> <given-names>J.</given-names></name> <name><surname>Paul</surname> <given-names>A.</given-names></name> <name><surname>Sarkar</surname> <given-names>R.</given-names></name> <name><surname>Khan</surname> <given-names>Z.</given-names></name> <name><surname>Banerjee</surname> <given-names>K.</given-names></name></person-group> (<year>2021</year>). <article-title>Anthocyanin profiling using UV-vis spectroscopy and liquid chromatography mass spectrometry.</article-title> <source><italic>J. AOAC Int.</italic></source> <volume>103</volume> <fpage>23</fpage>&#x2013;<lpage>39</lpage>. <pub-id pub-id-type="doi">10.5740/jaoacint.19-0201</pub-id> <pub-id pub-id-type="pmid">31462350</pub-id></citation></ref>
<ref id="B162"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Scandalios</surname> <given-names>J. G.</given-names></name></person-group> (<year>2002</year>). <article-title>Oxidative stress responses - What have genome-scale studies taught us?</article-title> <source><italic>Genome Biol.</italic></source> <volume>3</volume> <fpage>1</fpage>&#x2013;<lpage>6</lpage>. <pub-id pub-id-type="doi">10.1186/gb-2002-3-7-reviews1019</pub-id> <pub-id pub-id-type="pmid">12184812</pub-id></citation></ref>
<ref id="B163"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Schauer</surname> <given-names>N.</given-names></name> <name><surname>Semel</surname> <given-names>Y.</given-names></name> <name><surname>Roessner</surname> <given-names>U.</given-names></name> <name><surname>Gur</surname> <given-names>A.</given-names></name> <name><surname>Balbo</surname> <given-names>I.</given-names></name> <name><surname>Carrari</surname> <given-names>F.</given-names></name><etal/></person-group> (<year>2006</year>). <article-title>Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement.</article-title> <source><italic>Nat. Biotechnol.</italic></source> <volume>24</volume> <fpage>447</fpage>&#x2013;<lpage>454</lpage>. <pub-id pub-id-type="doi">10.1038/nbt1192</pub-id> <pub-id pub-id-type="pmid">16531992</pub-id></citation></ref>
<ref id="B164"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Schimmel</surname> <given-names>B. C. J.</given-names></name> <name><surname>Alba</surname> <given-names>J. M.</given-names></name> <name><surname>Wybouw</surname> <given-names>N.</given-names></name> <name><surname>Glas</surname> <given-names>J. J.</given-names></name> <name><surname>Meijer</surname> <given-names>T. T.</given-names></name> <name><surname>Schuurink</surname> <given-names>R. C.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Distinct signatures of host defense suppression by plant-feeding mites.</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>19</volume>:<issue>3265</issue>. <pub-id pub-id-type="doi">10.3390/ijms19103265</pub-id> <pub-id pub-id-type="pmid">30347842</pub-id></citation></ref>
<ref id="B165"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Schreiber</surname> <given-names>G.</given-names></name> <name><surname>Reuveni</surname> <given-names>M.</given-names></name> <name><surname>Evenor</surname> <given-names>D.</given-names></name> <name><surname>Oren-Shamir</surname> <given-names>M.</given-names></name> <name><surname>Ovadia</surname> <given-names>R.</given-names></name> <name><surname>Sapir-Mir</surname> <given-names>M.</given-names></name><etal/></person-group> (<year>2012</year>). <article-title>ANTHOCYANIN1 from Solanum chilense is more efficient in accumulating anthocyanin metabolites than its Solanum lycopersicum counterpart in association with the ANTHOCYANIN FRUIT phenotype of tomato.</article-title> <source><italic>Theor. Appl. Genet.</italic></source> <volume>124</volume> <fpage>295</fpage>&#x2013;<lpage>307</lpage>. <pub-id pub-id-type="doi">10.1007/s00122-011-1705-6</pub-id> <pub-id pub-id-type="pmid">21947299</pub-id></citation></ref>
<ref id="B166"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Schreurs</surname> <given-names>A. S.</given-names></name> <name><surname>Shirazi-Fard</surname> <given-names>Y.</given-names></name> <name><surname>Shahnazari</surname> <given-names>M.</given-names></name> <name><surname>Alwood</surname> <given-names>J. S.</given-names></name> <name><surname>Truong</surname> <given-names>T. A.</given-names></name> <name><surname>Tahimic</surname> <given-names>C. G. T.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Dried plum diet protects from bone loss caused by ionizing radiation.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>6</volume> <fpage>1</fpage>&#x2013;<lpage>11</lpage>. <pub-id pub-id-type="doi">10.1038/srep21343</pub-id> <pub-id pub-id-type="pmid">26867002</pub-id></citation></ref>
<ref id="B167"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Scranton</surname> <given-names>M. A.</given-names></name> <name><surname>Fowler</surname> <given-names>J. H.</given-names></name> <name><surname>Girke</surname> <given-names>T.</given-names></name> <name><surname>Walling</surname> <given-names>L. L.</given-names></name></person-group> (<year>2013</year>). <article-title>Microarray Analysis of Tomato&#x2019;s Early and Late Wound Response Reveals New Regulatory Targets for Leucine Aminopeptidase A.</article-title> <source><italic>PLoS One</italic></source> <volume>8</volume>:<issue>e77889</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0077889</pub-id> <pub-id pub-id-type="pmid">24205013</pub-id></citation></ref>
<ref id="B168"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>&#x015E;ensoy</surname> <given-names>&#x00CD;</given-names></name> <name><surname>Rosen</surname> <given-names>R. T.</given-names></name> <name><surname>Ho</surname> <given-names>C. T.</given-names></name> <name><surname>Karwe</surname> <given-names>M. V.</given-names></name></person-group> (<year>2006</year>). <article-title>Effect of processing on buckwheat phenolics and antioxidant activity.</article-title> <source><italic>Food Chem.</italic></source> <volume>99</volume> <fpage>388</fpage>&#x2013;<lpage>393</lpage>. <pub-id pub-id-type="doi">10.1016/j.foodchem.2005.08.007</pub-id></citation></ref>
<ref id="B169"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Serrato</surname> <given-names>A. J.</given-names></name> <name><surname>Fern&#x00E1;ndez-Trijueque</surname> <given-names>J.</given-names></name> <name><surname>Barajas-L&#x00F3;pez</surname> <given-names>J.</given-names></name> <name><surname>de</surname> <given-names>D.</given-names></name> <name><surname>Chueca</surname> <given-names>A.</given-names></name> <name><surname>Sahrawy</surname> <given-names>M.</given-names></name></person-group> (<year>2013</year>). <article-title>Plastid thioredoxins: a &#x201C;one-for-all&#x201D; redox-signaling system in plants.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>4</volume>:<issue>463</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2013.00463</pub-id> <pub-id pub-id-type="pmid">24319449</pub-id></citation></ref>
<ref id="B170"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sewelam</surname> <given-names>N.</given-names></name> <name><surname>Kazan</surname> <given-names>K.</given-names></name> <name><surname>Schenk</surname> <given-names>P. M.</given-names></name></person-group> (<year>2016</year>). <article-title>Global plant stress signaling: reactive oxygen species at the cross-road.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>7</volume>:<issue>187</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2016.00187</pub-id> <pub-id pub-id-type="pmid">26941757</pub-id></citation></ref>
<ref id="B171"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sharma</surname> <given-names>P.</given-names></name> <name><surname>Padh</surname> <given-names>H.</given-names></name> <name><surname>Shrivastava</surname> <given-names>N.</given-names></name></person-group> (<year>2013</year>). <article-title>Hairy root cultures: a suitable biological system for studying secondary metabolic pathways in plants.</article-title> <source><italic>Eng. Life Sci.</italic></source> <volume>13</volume> <fpage>62</fpage>&#x2013;<lpage>75</lpage>. <pub-id pub-id-type="doi">10.1002/elsc.201200030</pub-id></citation></ref>
<ref id="B172"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Shi</surname> <given-names>J.</given-names></name> <name><surname>Du</surname> <given-names>X.</given-names></name></person-group> (<year>2020</year>). <article-title>Identification, characterization and expression analysis of calmodulin and calmodulin-like proteins in Solanum pennellii.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>10</volume> <fpage>1</fpage>&#x2013;<lpage>17</lpage>. <pub-id pub-id-type="doi">10.1038/s41598-020-64178-y</pub-id> <pub-id pub-id-type="pmid">32366918</pub-id></citation></ref>
<ref id="B173"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Shi</surname> <given-names>R.</given-names></name> <name><surname>Panthee</surname> <given-names>D. R.</given-names></name></person-group> (<year>2020</year>). <article-title>Transcriptome-based analysis of tomato genotypes resistant to bacterial spot (Xanthomonas perforans) race t4.</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>21</volume> <fpage>1</fpage>&#x2013;<lpage>31</lpage>. <pub-id pub-id-type="doi">10.3390/ijms21114070</pub-id> <pub-id pub-id-type="pmid">32517212</pub-id></citation></ref>
<ref id="B174"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sol&#x00EC;s-Oviedo</surname> <given-names>R. L.</given-names></name> <name><surname>de La Cruz Pech-Canul</surname> <given-names>&#x00C1;</given-names></name></person-group> (<year>2019</year>). <source><italic>Frontiers and New Trends in the Science of Fermented Food and Beverages.</italic></source> <publisher-loc>London</publisher-loc>: <publisher-name>IntechOpen</publisher-name>. <pub-id pub-id-type="doi">10.5772/intechopen.73404</pub-id></citation></ref>
<ref id="B175"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Spelt</surname> <given-names>C.</given-names></name> <name><surname>Quattrocchio</surname> <given-names>F.</given-names></name> <name><surname>Mol</surname> <given-names>J. N. M.</given-names></name> <name><surname>Koes</surname> <given-names>R.</given-names></name></person-group> (<year>2000</year>). <article-title>anthocyanin1 of Petunia Encodes a Basic Helix-Loop-Helix Protein That Directly Activates Transcription of Structural Anthocyanin Genes.</article-title> <source><italic>Plant Cell</italic></source> <volume>12</volume>:<issue>1619</issue>. <pub-id pub-id-type="doi">10.2307/3871178</pub-id></citation></ref>
<ref id="B176"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Stracke</surname> <given-names>R.</given-names></name> <name><surname>Werber</surname> <given-names>M.</given-names></name> <name><surname>Weisshaar</surname> <given-names>B.</given-names></name></person-group> (<year>2001</year>). <article-title>The R2R3-MYB gene family in Arabidopsis thaliana.</article-title> <source><italic>Curr. Opin. Plant Biol.</italic></source> <volume>4</volume> <fpage>447</fpage>&#x2013;<lpage>456</lpage>. <pub-id pub-id-type="doi">10.1016/S1369-5266(00)00199-0</pub-id></citation></ref>
<ref id="B177"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Su</surname> <given-names>X.</given-names></name> <name><surname>Xu</surname> <given-names>J.</given-names></name> <name><surname>Rhodes</surname> <given-names>D.</given-names></name> <name><surname>Shen</surname> <given-names>Y.</given-names></name> <name><surname>Song</surname> <given-names>W.</given-names></name> <name><surname>Katz</surname> <given-names>B.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Identification and quantification of anthocyanins in transgenic purple tomato.</article-title> <source><italic>Food Chem.</italic></source> <volume>202</volume> <fpage>184</fpage>&#x2013;<lpage>188</lpage>. <pub-id pub-id-type="doi">10.1016/j.foodchem.2016.01.128</pub-id> <pub-id pub-id-type="pmid">26920283</pub-id></citation></ref>
<ref id="B178"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sui</surname> <given-names>X.</given-names></name> <name><surname>Sun</surname> <given-names>H.</given-names></name> <name><surname>Qi</surname> <given-names>B.</given-names></name> <name><surname>Zhang</surname> <given-names>M.</given-names></name> <name><surname>Li</surname> <given-names>Y.</given-names></name> <name><surname>Jiang</surname> <given-names>L.</given-names></name></person-group> (<year>2018</year>). <article-title>Functional and conformational changes to soy proteins accompanying anthocyanins: focus on covalent and non-covalent interactions.</article-title> <source><italic>Food Chem.</italic></source> <volume>245</volume> <fpage>871</fpage>&#x2013;<lpage>878</lpage>. <pub-id pub-id-type="doi">10.1016/j.foodchem.2017.11.090</pub-id> <pub-id pub-id-type="pmid">29287453</pub-id></citation></ref>
<ref id="B179"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sun</surname> <given-names>C.</given-names></name> <name><surname>Deng</surname> <given-names>L.</given-names></name> <name><surname>Du</surname> <given-names>M.</given-names></name> <name><surname>Zhao</surname> <given-names>J.</given-names></name> <name><surname>Chen</surname> <given-names>Q.</given-names></name> <name><surname>Huang</surname> <given-names>T.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>A Transcriptional Network Promotes Anthocyanin Biosynthesis in Tomato Flesh.</article-title> <source><italic>Mol. Plant</italic></source> <volume>13</volume> <fpage>42</fpage>&#x2013;<lpage>58</lpage>. <pub-id pub-id-type="doi">10.1016/j.molp.2019.10.010</pub-id> <pub-id pub-id-type="pmid">31678614</pub-id></citation></ref>
<ref id="B180"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sun</surname> <given-names>X.</given-names></name> <name><surname>Shu</surname> <given-names>J.</given-names></name> <name><surname>Mohamed</surname> <given-names>A. M. A.</given-names></name> <name><surname>Deng</surname> <given-names>X.</given-names></name> <name><surname>Zhi</surname> <given-names>X.</given-names></name> <name><surname>Bai</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Identification and characterization of EI (elongated internode) gene in tomato (solanum lycopersicum).</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>20</volume> <fpage>1</fpage>&#x2013;<lpage>18</lpage>. <pub-id pub-id-type="doi">10.3390/ijms20092204</pub-id> <pub-id pub-id-type="pmid">31060285</pub-id></citation></ref>
<ref id="B181"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sundaresan</surname> <given-names>S.</given-names></name> <name><surname>Philosoph-Hadas</surname> <given-names>S.</given-names></name> <name><surname>Riov</surname> <given-names>J.</given-names></name> <name><surname>Mugasimangalam</surname> <given-names>R.</given-names></name> <name><surname>Kuravadi</surname> <given-names>N. A.</given-names></name> <name><surname>Kochanek</surname> <given-names>B.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>De novo transcriptome sequencing and development of abscission zone-specific microarray as a new molecular tool for analysis of tomato organ abscission.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>6</volume>:<issue>1258</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2015.01258</pub-id> <pub-id pub-id-type="pmid">26834766</pub-id></citation></ref>
<ref id="B182"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Takos</surname> <given-names>A. M.</given-names></name> <name><surname>Jaff&#x00E9;</surname> <given-names>F. W.</given-names></name> <name><surname>Jacob</surname> <given-names>S. R.</given-names></name> <name><surname>Bogs</surname> <given-names>J.</given-names></name> <name><surname>Robinson</surname> <given-names>S. P.</given-names></name> <name><surname>Walker</surname> <given-names>A. R.</given-names></name></person-group> (<year>2006</year>). <article-title>Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>142</volume> <fpage>1216</fpage>&#x2013;<lpage>1232</lpage>. <pub-id pub-id-type="doi">10.1104/pp.106.088104</pub-id> <pub-id pub-id-type="pmid">17012405</pub-id></citation></ref>
<ref id="B183"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Taylor</surname> <given-names>B. H.</given-names></name> <name><surname>Scheuring</surname> <given-names>C. F.</given-names></name></person-group> (<year>1994</year>). <article-title>A molecular marker for lateral root initiation: the RSI-1 gene of tomato (Lycopersicon esculentum Mill) is activated in early lateral root primordia.</article-title> <source><italic>Mol. Gener. Genet.</italic></source> <volume>243</volume> <fpage>148</fpage>&#x2013;<lpage>157</lpage>. <pub-id pub-id-type="doi">10.1007/BF00280311</pub-id> <pub-id pub-id-type="pmid">8177211</pub-id></citation></ref>
<ref id="B184"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Thamaphat</surname> <given-names>K.</given-names></name> <name><surname>Goodman</surname> <given-names>B. A.</given-names></name> <name><surname>Limsuwan</surname> <given-names>P.</given-names></name> <name><surname>Smith</surname> <given-names>S. M.</given-names></name></person-group> (<year>2015</year>). <article-title>Rapid screening for anthocyanins in cane sugars using ESR spectroscopy.</article-title> <source><italic>Food Chem.</italic></source> <volume>171</volume> <fpage>123</fpage>&#x2013;<lpage>127</lpage>. <pub-id pub-id-type="doi">10.1016/j.foodchem.2014.08.126</pub-id> <pub-id pub-id-type="pmid">25308651</pub-id></citation></ref>
<ref id="B185"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Thwe</surname> <given-names>A.</given-names></name> <name><surname>Arasu</surname> <given-names>M. V.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Park</surname> <given-names>C. H.</given-names></name> <name><surname>Kim</surname> <given-names>S. J.</given-names></name> <name><surname>Al-Dhabi</surname> <given-names>N. A.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Effect of different Agrobacterium rhizogenes strains on hairy root induction and phenylpropanoid biosynthesis in tartary buckwheat (Fagopyrum tataricum Gaertn).</article-title> <source><italic>Front. Microbiol.</italic></source> <volume>7</volume>:<issue>318</issue>. <pub-id pub-id-type="doi">10.3389/fmicb.2016.00318</pub-id> <pub-id pub-id-type="pmid">27014239</pub-id></citation></ref>
<ref id="B186"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tian</surname> <given-names>L.</given-names></name> <name><surname>Tan</surname> <given-names>Y.</given-names></name> <name><surname>Chen</surname> <given-names>G.</given-names></name> <name><surname>Wang</surname> <given-names>G.</given-names></name> <name><surname>Sun</surname> <given-names>J.</given-names></name> <name><surname>Ou</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Metabolism of anthocyanins and consequent effects on the gut microbiota.</article-title> <source><italic>Crit. Rev. Food Sci. Nutr.</italic></source> <volume>59</volume> <fpage>982</fpage>&#x2013;<lpage>991</lpage>. <pub-id pub-id-type="doi">10.1080/10408398.2018.1533517</pub-id> <pub-id pub-id-type="pmid">30595029</pub-id></citation></ref>
<ref id="B187"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tohge</surname> <given-names>T.</given-names></name> <name><surname>de Souza</surname> <given-names>L. P.</given-names></name> <name><surname>Fernie</surname> <given-names>A. R.</given-names></name></person-group> (<year>2017</year>). <article-title>Current understanding of the pathways of flavonoid biosynthesis in model and crop plants.</article-title> <source><italic>J. Exp. Bot.</italic></source> <volume>68</volume> <fpage>4013</fpage>&#x2013;<lpage>4028</lpage>. <pub-id pub-id-type="doi">10.1093/jxb/erx177</pub-id> <pub-id pub-id-type="pmid">28922752</pub-id></citation></ref>
<ref id="B188"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tohge</surname> <given-names>T.</given-names></name> <name><surname>Scossa</surname> <given-names>F.</given-names></name> <name><surname>Wendenburg</surname> <given-names>R.</given-names></name> <name><surname>Frasse</surname> <given-names>P.</given-names></name> <name><surname>Balbo</surname> <given-names>I.</given-names></name> <name><surname>Watanabe</surname> <given-names>M.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex.</article-title> <source><italic>Mol. Plant</italic></source> <volume>13</volume> <fpage>1027</fpage>&#x2013;<lpage>1046</lpage>. <pub-id pub-id-type="doi">10.1016/j.molp.2020.04.004</pub-id> <pub-id pub-id-type="pmid">32305499</pub-id></citation></ref>
<ref id="B189"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tominaga-Wada</surname> <given-names>R.</given-names></name> <name><surname>Nukumizu</surname> <given-names>Y.</given-names></name> <name><surname>Wada</surname> <given-names>T.</given-names></name></person-group> (<year>2013</year>). <article-title>Tomato (Solanum lycopersicum) homologs of TRIPTYCHON (SLTRY) and GLABRA3 (SLGL3) are involved in anthocyanin accumulation.</article-title> <source><italic>Plant Signal. Behav.</italic></source> <volume>8</volume> <fpage>8</fpage>&#x2013;<lpage>10</lpage>. <pub-id pub-id-type="doi">10.4161/psb.24575</pub-id> <pub-id pub-id-type="pmid">23603939</pub-id></citation></ref>
<ref id="B190"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tuner</surname> <given-names>H.</given-names></name> <name><surname>Korkmaz</surname> <given-names>M.</given-names></name></person-group> (<year>2007</year>). <article-title>Radiostability of butylated hydroxytoluene (BHT): an ESR study.</article-title> <source><italic>Nuclear Instr. Methods Phys. Res. B Beam Interact. Mater. Atoms</italic></source> <volume>258</volume> <fpage>388</fpage>&#x2013;<lpage>394</lpage>. <pub-id pub-id-type="doi">10.1016/j.nimb.2007.02.098</pub-id></citation></ref>
<ref id="B191"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tzin</surname> <given-names>V.</given-names></name> <name><surname>Rogachev</surname> <given-names>I.</given-names></name> <name><surname>Meir</surname> <given-names>S.</given-names></name> <name><surname>Moyal Ben Zvi</surname> <given-names>M.</given-names></name> <name><surname>Masci</surname> <given-names>T.</given-names></name> <name><surname>Vainstein</surname> <given-names>A.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Altered Levels of Aroma and Volatiles by Metabolic Engineering of Shikimate Pathway Genes in Tomato Fruits.</article-title> <source><italic>AIMS Bioeng.</italic></source> <volume>2</volume> <fpage>75</fpage>&#x2013;<lpage>92</lpage>. <pub-id pub-id-type="doi">10.3934/bioeng.2015.2.75</pub-id></citation></ref>
<ref id="B192"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>van Hoeck</surname> <given-names>A.</given-names></name> <name><surname>Horemans</surname> <given-names>N.</given-names></name> <name><surname>Nauts</surname> <given-names>R.</given-names></name> <name><surname>van Hees</surname> <given-names>M.</given-names></name> <name><surname>Vandenhove</surname> <given-names>H.</given-names></name> <name><surname>Blust</surname> <given-names>R.</given-names></name></person-group> (<year>2017</year>). <article-title>Lemna minor plants chronically exposed to ionising radiation: rNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies.</article-title> <source><italic>Plant Sci.</italic></source> <volume>257</volume> <fpage>84</fpage>&#x2013;<lpage>95</lpage>. <pub-id pub-id-type="doi">10.1016/j.plantsci.2017.01.010</pub-id> <pub-id pub-id-type="pmid">28224921</pub-id></citation></ref>
<ref id="B193"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>van Kan</surname> <given-names>J. A. L.</given-names></name> <name><surname>Joosten</surname> <given-names>M. H. A. J.</given-names></name> <name><surname>Wagemakers</surname> <given-names>C. A. M.</given-names></name> <name><surname>van den Berg-Velthuis</surname> <given-names>G. C. M.</given-names></name> <name><surname>de Wit</surname> <given-names>P. J. G. M.</given-names></name></person-group> (<year>1992</year>). <article-title>Differential accumulation of mRNAs encoding extracellular and intracellular PR proteins in tomato induced by virulent and avirulent races of Cladosporium fulvum.</article-title> <source><italic>Plant Mol. Biol.</italic></source> <volume>20</volume> <fpage>513</fpage>&#x2013;<lpage>527</lpage>. <pub-id pub-id-type="doi">10.1007/BF00040610</pub-id> <pub-id pub-id-type="pmid">1421154</pub-id></citation></ref>
<ref id="B194"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Vandenhove</surname> <given-names>H.</given-names></name> <name><surname>Vanhoudt</surname> <given-names>N.</given-names></name> <name><surname>Cuypers</surname> <given-names>A.</given-names></name> <name><surname>van Hees</surname> <given-names>M.</given-names></name> <name><surname>Wannijn</surname> <given-names>J.</given-names></name> <name><surname>Horemans</surname> <given-names>N.</given-names></name></person-group> (<year>2010</year>). <article-title>Life-cycle chronic gamma exposure of Arabidopsis thaliana induces growth effects but no discernable effects on oxidative stress pathways.</article-title> <source><italic>Plant Physiol. Biochem.</italic></source> <volume>48</volume> <fpage>778</fpage>&#x2013;<lpage>786</lpage>. <pub-id pub-id-type="doi">10.1016/j.plaphy.2010.06.006</pub-id> <pub-id pub-id-type="pmid">20637647</pub-id></citation></ref>
<ref id="B195"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Vardhan</surname> <given-names>P. V.</given-names></name> <name><surname>Shukla</surname> <given-names>L. I.</given-names></name></person-group> (<year>2017</year>). <article-title>Gamma irradiation of medicinally important plants and the enhancement of secondary metabolite production.</article-title> <source><italic>Int. J. Radiat. Biol.</italic></source> <volume>93</volume> <fpage>967</fpage>&#x2013;<lpage>979</lpage>. <pub-id pub-id-type="doi">10.1080/09553002.2017.1344788</pub-id> <pub-id pub-id-type="pmid">28714761</pub-id></citation></ref>
<ref id="B196"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Vel&#x00E1;zquez-M&#x00E1;rquez</surname> <given-names>S.</given-names></name> <name><surname>De-La-Cruz</surname> <given-names>I. M.</given-names></name> <name><surname>Tapia-L&#x00F3;pez</surname> <given-names>R.</given-names></name> <name><surname>N&#x00FA;&#x00F1;ez-Farf&#x00E1;n</surname> <given-names>J.</given-names></name></person-group> (<year>2021</year>). <article-title>Tropane alkaloids and terpenes synthase genes of Datura stramonium (Solanaceae).</article-title> <source><italic>PeerJ.</italic></source> <volume>9</volume>:<issue>e11466</issue>. <pub-id pub-id-type="doi">10.7717/peerj.11466</pub-id> <pub-id pub-id-type="pmid">34178440</pub-id></citation></ref>
<ref id="B197"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Verweij</surname> <given-names>W.</given-names></name> <name><surname>Spelt</surname> <given-names>C.</given-names></name> <name><surname>Di Sansebastiano</surname> <given-names>G. P.</given-names></name> <name><surname>Vermeer</surname> <given-names>J.</given-names></name> <name><surname>Reale</surname> <given-names>L.</given-names></name> <name><surname>Ferranti</surname> <given-names>F.</given-names></name><etal/></person-group> (<year>2008</year>). <article-title>An H+ P-ATPase on the tonoplast determines vacuolar pH and flower colour.</article-title> <source><italic>Nat. Cell Biol.</italic></source> <volume>10</volume> <fpage>1456</fpage>&#x2013;<lpage>1462</lpage>. <pub-id pub-id-type="doi">10.1038/ncb1805</pub-id> <pub-id pub-id-type="pmid">18997787</pub-id></citation></ref>
<ref id="B198"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Verweij</surname> <given-names>W.</given-names></name> <name><surname>Spelt</surname> <given-names>C. E.</given-names></name> <name><surname>Bliek</surname> <given-names>M.</given-names></name> <name><surname>de Vries</surname> <given-names>M.</given-names></name> <name><surname>Wit</surname> <given-names>N.</given-names></name> <name><surname>Faraco</surname> <given-names>M.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Functionally similar WRKY proteins regulate vacuolar acidification in petunia and hair development in arabidopsis.</article-title> <source><italic>Plant Cell</italic></source> <volume>28</volume> <fpage>786</fpage>&#x2013;<lpage>803</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.15.00608</pub-id> <pub-id pub-id-type="pmid">26977085</pub-id></citation></ref>
<ref id="B199"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Villani</surname> <given-names>M. E.</given-names></name> <name><surname>Massa</surname> <given-names>S.</given-names></name> <name><surname>Lopresto</surname> <given-names>V.</given-names></name> <name><surname>Pinto</surname> <given-names>R.</given-names></name> <name><surname>Salzano</surname> <given-names>A. M.</given-names></name> <name><surname>Scaloni</surname> <given-names>A.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Effects of high-intensity static magnetic fields on a root-based bioreactor system for space applications.</article-title> <source><italic>Life Sci. Space Res.</italic></source> <volume>15</volume> <fpage>79</fpage>&#x2013;<lpage>87</lpage>. <pub-id pub-id-type="doi">10.1016/j.lssr.2017.09.002</pub-id> <pub-id pub-id-type="pmid">29198317</pub-id></citation></ref>
<ref id="B200"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Vivar-Quintana</surname> <given-names>A. M.</given-names></name> <name><surname>Santos-Buelga</surname> <given-names>C.</given-names></name> <name><surname>Rivas-Gonzalo</surname> <given-names>J. C.</given-names></name></person-group> (<year>2002</year>). <article-title>Anthocyanin-derived pigments and colour of red wines.</article-title> <source><italic>Anal. Chim. Acta</italic></source> <volume>458</volume> <fpage>147</fpage>&#x2013;<lpage>155</lpage>. <pub-id pub-id-type="doi">10.1016/S0003-2670(01)01619-1</pub-id></citation></ref>
<ref id="B201"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>T.</given-names></name> <name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Zhu</surname> <given-names>H.</given-names></name></person-group> (<year>2019</year>). <article-title>CRISPR technology is revolutionizing the improvement of tomato and other fruit crops.</article-title> <source><italic>Hortic. Res.</italic></source> <volume>6</volume>:<issue>77</issue>. <pub-id pub-id-type="doi">10.1038/s41438-019-0159-x</pub-id> <pub-id pub-id-type="pmid">31240102</pub-id></citation></ref>
<ref id="B202"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>T. W.</given-names></name> <name><surname>Lu</surname> <given-names>L.</given-names></name> <name><surname>Wang</surname> <given-names>D.</given-names></name> <name><surname>Thompson</surname> <given-names>J. E.</given-names></name></person-group> (<year>2001</year>). <article-title>Isolation and Characterization of Senescence-induced cDNAs Encoding Deoxyhypusine Synthase and Eucaryotic Translation Initiation Factor 5A from Tomato.</article-title> <source><italic>J. Biol. Chem.</italic></source> <volume>276</volume> <fpage>17541</fpage>&#x2013;<lpage>17549</lpage>. <pub-id pub-id-type="doi">10.1074/jbc.M008544200</pub-id> <pub-id pub-id-type="pmid">11278418</pub-id></citation></ref>
<ref id="B203"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wen</surname> <given-names>B.</given-names></name> <name><surname>Zhang</surname> <given-names>F.</given-names></name> <name><surname>Wu</surname> <given-names>X.</given-names></name> <name><surname>Li</surname> <given-names>H.</given-names></name></person-group> (<year>2020</year>). <article-title>Characterization of the Tomato (Solanum lycopersicum) Pectin Methylesterases: evolution, Activity of Isoforms and Expression During Fruit Ripening.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>11</volume>:<issue>238</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2020.00238</pub-id> <pub-id pub-id-type="pmid">32194610</pub-id></citation></ref>
<ref id="B204"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Williams</surname> <given-names>R. J.</given-names></name> <name><surname>Spencer</surname> <given-names>J. P. E.</given-names></name> <name><surname>Rice-Evans</surname> <given-names>C.</given-names></name></person-group> (<year>2004</year>). <article-title>Flavonoids: antioxidants or signalling molecules?</article-title> <source><italic>Free Radic. Biol. Med.</italic></source> <volume>36</volume> <fpage>838</fpage>&#x2013;<lpage>849</lpage>. <pub-id pub-id-type="doi">10.1016/j.freeradbiomed.2004.01.001</pub-id> <pub-id pub-id-type="pmid">15019969</pub-id></citation></ref>
<ref id="B205"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wolff</surname> <given-names>S. A.</given-names></name> <name><surname>Coelho</surname> <given-names>L. H.</given-names></name> <name><surname>Karoliussen</surname> <given-names>I.</given-names></name> <name><surname>Jost</surname> <given-names>A. I. K.</given-names></name></person-group> (<year>2014</year>). <article-title>Effects of the extraterrestrial environment on plants: recommendations for future space experiments for the MELiSSA higher plant compartment.</article-title> <source><italic>Life</italic></source> <volume>4</volume> <fpage>189</fpage>&#x2013;<lpage>204</lpage>. <pub-id pub-id-type="doi">10.3390/life4020189</pub-id> <pub-id pub-id-type="pmid">25370192</pub-id></citation></ref>
<ref id="B206"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yan</surname> <given-names>L.</given-names></name> <name><surname>Zhai</surname> <given-names>Q.</given-names></name> <name><surname>Wei</surname> <given-names>J.</given-names></name> <name><surname>Li</surname> <given-names>S.</given-names></name> <name><surname>Wang</surname> <given-names>B.</given-names></name> <name><surname>Huang</surname> <given-names>T.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>Role of Tomato Lipoxygenase D in Wound-Induced Jasmonate Biosynthesis and Plant Immunity to Insect Herbivores.</article-title> <source><italic>PLoS Genet.</italic></source> <volume>9</volume>:<issue>e1003964</issue>. <pub-id pub-id-type="doi">10.1371/journal.pgen.1003964</pub-id> <pub-id pub-id-type="pmid">24348260</pub-id></citation></ref>
<ref id="B207"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yan</surname> <given-names>S.</given-names></name> <name><surname>Chen</surname> <given-names>N.</given-names></name> <name><surname>Huang</surname> <given-names>Z.</given-names></name> <name><surname>Li</surname> <given-names>D.</given-names></name> <name><surname>Zhi</surname> <given-names>J.</given-names></name> <name><surname>Yu</surname> <given-names>B.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Anthocyanin Fruit encodes an R2R3-MYB transcription factor, SlAN2-like, activating the transcription of SlMYBATV to fine-tune anthocyanin content in tomato fruit.</article-title> <source><italic>New Phytol.</italic></source> <volume>225</volume> <fpage>2048</fpage>&#x2013;<lpage>2063</lpage>.</citation></ref>
<ref id="B208"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname> <given-names>H.</given-names></name> <name><surname>Xiao</surname> <given-names>X.</given-names></name> <name><surname>Zhao</surname> <given-names>X.</given-names></name> <name><surname>Wu</surname> <given-names>Y.</given-names></name></person-group> (<year>2015</year>). &#x201C;<article-title>Intrinsic Fluorescence Spectra of Tryptophan. Tyrosine and Phenyloalanine</article-title>&#x201D; in <source><italic>Proceedings of the 5th International Conference on Advanced Design and Manufacturing Engineering.</italic></source> (<publisher-loc>Netherlands</publisher-loc>: <publisher-name>Atlantis Press</publisher-name>). <fpage>224</fpage>&#x2013;<lpage>233</lpage>. <pub-id pub-id-type="doi">10.2991/icadme-15.2015.46</pub-id> <pub-id pub-id-type="pmid">32175718</pub-id></citation></ref>
<ref id="B209"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname> <given-names>Y. X.</given-names></name> <name><surname>Wang</surname> <given-names>M. M.</given-names></name> <name><surname>Yin</surname> <given-names>Y. L.</given-names></name> <name><surname>Onac</surname> <given-names>E.</given-names></name> <name><surname>Zhou</surname> <given-names>G. F.</given-names></name> <name><surname>Peng</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>RNA-seq analysis reveals the role of red light in resistance against <italic>Pseudomonas</italic> syringae pv. tomato DC3000 in tomato plants.</article-title> <source><italic>BMC Genomics</italic></source> <volume>16</volume>:<issue>120</issue>. <pub-id pub-id-type="doi">10.1186/s12864-015-1228-7</pub-id> <pub-id pub-id-type="pmid">25765075</pub-id></citation></ref>
<ref id="B210"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zabel</surname> <given-names>P.</given-names></name> <name><surname>Bamsey</surname> <given-names>M.</given-names></name> <name><surname>Schubert</surname> <given-names>D.</given-names></name> <name><surname>Tajmar</surname> <given-names>M.</given-names></name></person-group> (<year>2016</year>). <article-title>Review and analysis of over 40 years of space plant growth systems.</article-title> <source><italic>Life Sci. Space Res.</italic></source> <volume>10</volume> <fpage>1</fpage>&#x2013;<lpage>16</lpage>. <pub-id pub-id-type="doi">10.1016/j.lssr.2016.06.004</pub-id> <pub-id pub-id-type="pmid">27662782</pub-id></citation></ref>
<ref id="B211"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zabel</surname> <given-names>P.</given-names></name> <name><surname>Bamsey</surname> <given-names>M.</given-names></name> <name><surname>Zeidler</surname> <given-names>C.</given-names></name> <name><surname>Vrakking</surname> <given-names>V.</given-names></name> <name><surname>Johannes</surname> <given-names>B.</given-names></name> <name><surname>Rettberg</surname> <given-names>P.</given-names></name></person-group> (<year>2015</year>). &#x201C;<article-title>Introducing EDEN ISS - A European project on advancing plant cultivation technologies and operations</article-title>,&#x201D; in <source><italic>45th International Conference on Environmental Systems.</italic></source></citation></ref>
<ref id="B212"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Koes</surname> <given-names>R.</given-names></name> <name><surname>Shang</surname> <given-names>H.</given-names></name> <name><surname>Fu</surname> <given-names>Z.</given-names></name> <name><surname>Wang</surname> <given-names>L.</given-names></name> <name><surname>Dong</surname> <given-names>X.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Identification and functional analysis of three new anthocyanin R2R3-MYB genes in Petunia.</article-title> <source><italic>Plant Dir</italic></source> <volume>3</volume> <fpage>1</fpage>&#x2013;<lpage>13</lpage>. <pub-id pub-id-type="doi">10.1002/pld3.114</pub-id> <pub-id pub-id-type="pmid">31245756</pub-id></citation></ref>
<ref id="B213"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Butelli</surname> <given-names>E.</given-names></name> <name><surname>Alseekh</surname> <given-names>S.</given-names></name> <name><surname>Tohge</surname> <given-names>T.</given-names></name> <name><surname>Rallapalli</surname> <given-names>G.</given-names></name> <name><surname>Luo</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato.</article-title> <source><italic>Nat. Commun</italic></source> <volume>6</volume> <fpage>1</fpage>&#x2013;<lpage>11</lpage>. <pub-id pub-id-type="doi">10.1038/ncomms9635</pub-id> <pub-id pub-id-type="pmid">26497596</pub-id></citation></ref>
<ref id="B214"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Butelli</surname> <given-names>E.</given-names></name> <name><surname>de Stefano</surname> <given-names>R.</given-names></name> <name><surname>Schoonbeek</surname> <given-names>H. J.</given-names></name> <name><surname>Magusin</surname> <given-names>A.</given-names></name> <name><surname>Pagliarani</surname> <given-names>C.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>Anthocyanins double the shelf life of tomatoes by delaying overripening and reducing susceptibility to gray mold.</article-title> <source><italic>Curr. Biol.</italic></source> <volume>23</volume> <fpage>1094</fpage>&#x2013;<lpage>1100</lpage>. <pub-id pub-id-type="doi">10.1016/j.cub.2013.04.072</pub-id> <pub-id pub-id-type="pmid">23707429</pub-id></citation></ref>
<ref id="B215"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Butelli</surname> <given-names>E.</given-names></name> <name><surname>Martin</surname> <given-names>C.</given-names></name></person-group> (<year>2014</year>). <article-title>Engineering anthocyanin biosynthesis in plants.</article-title> <source><italic>Curr. Opin. Plant Biol.</italic></source> <volume>19</volume> <fpage>81</fpage>&#x2013;<lpage>90</lpage>. <pub-id pub-id-type="doi">10.1016/j.pbi.2014.05.011</pub-id> <pub-id pub-id-type="pmid">24907528</pub-id></citation></ref>
<ref id="B216"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Song</surname> <given-names>H.</given-names></name> <name><surname>Wang</surname> <given-names>X.</given-names></name> <name><surname>Zhou</surname> <given-names>X.</given-names></name> <name><surname>Zhang</surname> <given-names>K.</given-names></name> <name><surname>Chen</surname> <given-names>X.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>The roles of different types of trichomes in tomato resistance to cold, drought, whiteflies, and botrytis.</article-title> <source><italic>Agronomy</italic></source> <volume>10</volume>:<issue>411</issue>. <pub-id pub-id-type="doi">10.3390/agronomy10030411</pub-id></citation></ref>
<ref id="B217"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhao</surname> <given-names>X.</given-names></name> <name><surname>Liu</surname> <given-names>Y.</given-names></name> <name><surname>Liu</surname> <given-names>X.</given-names></name> <name><surname>Jiang</surname> <given-names>J.</given-names></name></person-group> (<year>2018</year>). <article-title>Comparative transcriptome profiling of two tomato genotypes in response to potassium-deficiency stress.</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>19</volume>:<issue>2402</issue>. <pub-id pub-id-type="doi">10.3390/ijms19082402</pub-id> <pub-id pub-id-type="pmid">30110976</pub-id></citation></ref>
<ref id="B218"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zimmermann</surname> <given-names>I. M.</given-names></name> <name><surname>Heim</surname> <given-names>M. A.</given-names></name> <name><surname>Weisshaar</surname> <given-names>B.</given-names></name> <name><surname>Uhrig</surname> <given-names>J. F.</given-names></name></person-group> (<year>2004</year>). <article-title>Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins.</article-title> <source><italic>Plant J.</italic></source> <volume>40</volume> <fpage>22</fpage>&#x2013;<lpage>34</lpage>. <pub-id pub-id-type="doi">10.1111/j.1365-313X.2004.02183.x</pub-id> <pub-id pub-id-type="pmid">15361138</pub-id></citation></ref>
<ref id="B219"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zouari</surname> <given-names>I.</given-names></name> <name><surname>Salvioli</surname> <given-names>A.</given-names></name> <name><surname>Chialva</surname> <given-names>M.</given-names></name> <name><surname>Novero</surname> <given-names>M.</given-names></name> <name><surname>Miozzi</surname> <given-names>L.</given-names></name> <name><surname>Tenore</surname> <given-names>G. C.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>From root to fruit: rNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism.</article-title> <source><italic>BMC Genomics</italic></source> <volume>15</volume>:<issue>221</issue>. <pub-id pub-id-type="doi">10.1186/1471-2164-15-221</pub-id> <pub-id pub-id-type="pmid">24655934</pub-id></citation></ref>
</ref-list>
<fn-group>
<fn id="footnote1">
<label>1</label>
<p><ext-link ext-link-type="uri" xlink:href="https://github.com/KoesGroup/Snakemake_hisat-DESeq">https://github.com/KoesGroup/Snakemake_hisat-DESeq</ext-link></p></fn>
<fn id="footnote2">
<label>2</label>
<p><ext-link ext-link-type="uri" xlink:href="http://broadinstitute.github.io/picard/">http://broadinstitute.github.io/picard/</ext-link></p></fn>
<fn id="footnote3">
<label>3</label>
<p><ext-link ext-link-type="uri" xlink:href="https://ggplot2.tidyverse.org/">https://ggplot2.tidyverse.org/</ext-link></p></fn>
</fn-group>
</back>
</article>