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<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.2021.807448</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>Molecular Characterization Revealed the Role of Thaumatin-Like Proteins of Bread Wheat in Stress Response</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Sharma</surname> <given-names>Alok</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/969294/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Sharma</surname> <given-names>Himanshu</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/635659/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Rajput</surname> <given-names>Ruchika</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Pandey</surname> <given-names>Ashutosh</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1240442/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Upadhyay</surname> <given-names>Santosh Kumar</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/351646/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department of Botany, Panjab University</institution>, <addr-line>Chandigarh</addr-line>, <country>India</country></aff>
<aff id="aff2"><sup>2</sup><institution>Department of Biotechnology, I.K. Gujral Punjab Technical University</institution>, <addr-line>Jalandhar</addr-line>, <country>India</country></aff>
<aff id="aff3"><sup>3</sup><institution>National Institute of Plant Genome Research</institution>, <addr-line>New Delhi</addr-line>, <country>India</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Carla Pinheiro, New University of Lisbon, Portugal</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Zahoor Ahmad Mir, Indian Council of Agricultural Research, India; Sajad Ali, Yeungnam University, South Korea; Ertugrul Filiz, Duzce University, Turkey</p></fn>
<corresp id="c001">&#x002A;Correspondence: Santosh Kumar Upadhyay, <email>skupadhyay@pu.ac.in</email></corresp>
<fn fn-type="other" id="fn004"><p>This article was submitted to Plant Abiotic Stress, a section of the journal Frontiers in Plant Science</p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>11</day>
<month>01</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>12</volume>
<elocation-id>807448</elocation-id>
<history>
<date date-type="received">
<day>02</day>
<month>11</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>13</day>
<month>12</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2022 Sharma, Sharma, Rajput, Pandey and Upadhyay.</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Sharma, Sharma, Rajput, Pandey and Upadhyay</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>Thaumatin-like proteins (TLPs) are related to pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93 <italic>TLP</italic> genes were identified in the genome of <italic>Triticum aestivum.</italic> Further, we identified 26, 27, 39, and 37 <italic>TLP</italic> genes in the <italic>Brachypodium distachyon</italic>, <italic>Oryza sativa</italic>, <italic>Sorghum bicolor</italic>, and <italic>Zea mays</italic> genomes for comparative characterization, respectively. They could be grouped into small and long TLPs with conserved thaumatin signature motif. Tightly clustered genes exhibited conserved gene and protein structure. The physicochemical analyses suggested significant differences between small and long TLPs. Evolutionary analyses suggested the role of duplication events and purifying selection in the expansion of the TLP gene family. Expression analyses revealed the possible roles of <italic>TLPs</italic> in plant development and abiotic and fungal stress response. Recombinant expression of <italic>TaTLP2-B</italic> in <italic>Saccharomyces cerevisiae</italic> provided significant tolerance against cold, heat, osmotic, and salt stresses. The results depicted the importance of TLPs in cereal crops that would be highly useful in future crop improvement programs.</p>
</abstract>
<kwd-group>
<kwd>abiotic stress</kwd>
<kwd>biotic stress</kwd>
<kwd>cereals</kwd>
<kwd>thaumatin-like proteins</kwd>
<kwd><italic>TaTLP2-B</italic></kwd>
</kwd-group>
<counts>
<fig-count count="9"/>
<table-count count="3"/>
<equation-count count="0"/>
<ref-count count="85"/>
<page-count count="18"/>
<word-count count="11997"/>
</counts>
</article-meta>
</front>
<body>
<sec id="S1" sec-type="intro">
<title>Introduction</title>
<p>The growth and development of plants have always been affected by various abiotic and biotic stress conditions. In response to these stress conditions, plants produce numerous molecules including pathogenesis-related (PR) proteins (<xref ref-type="bibr" rid="B32">Kombrink and Somssich, 1997</xref>). PR proteins belong to a superfamily of defense-related proteins consisting of PR1-PR17 protein families that have been classified based on amino acid sequences, serological reaction, enzymatic activity, and so on (<xref ref-type="bibr" rid="B7">Christensen et al., 2002</xref>; <xref ref-type="bibr" rid="B74">van Loon et al., 2006</xref>).</p>
<p>Thaumatin-like proteins (TLPs) are related to the PR5 family of the PR superfamily (<xref ref-type="bibr" rid="B74">van Loon et al., 2006</xref>). These are called TLPs due to their significant similarity with a &#x223C;23 kDa sweet-tasting protein known as thaumatin (<xref ref-type="bibr" rid="B75">Velazhahan et al., 1999</xref>). Thaumatin protein was first isolated from an African shrub known as <italic>Thaumatococcus danielli</italic> (<xref ref-type="bibr" rid="B73">van der Wel and Loeve, 1972</xref>). Over the period, TLPs have been reported in a diverse group of organisms including insects, nematodes, fungi, and plants (<xref ref-type="bibr" rid="B60">Sakamoto et al., 2006</xref>; <xref ref-type="bibr" rid="B67">Shatters et al., 2006</xref>; <xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>; <xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>). In plants, TLPs are reported from algae to angiosperms (<xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>,<xref ref-type="bibr" rid="B40">b</xref>; <xref ref-type="bibr" rid="B56">Petre et al., 2011</xref>; <xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>).</p>
<p>Based on the molecular weight (MW), TLP proteins are grouped as long (L-type) and small (S-type) TLPs, having the MW of &#x223C;21&#x2013;26 kDa and &#x223C;16&#x2013;17 kDa, respectively. Long TLPs have been identified from each group of plants, while small TLPs are confined to only gymnospermous and monocot plants (<xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>,<xref ref-type="bibr" rid="B40">b</xref>; <xref ref-type="bibr" rid="B56">Petre et al., 2011</xref>; <xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>). A total of 16 and 10 conserved cysteine residues, forming eight and five disulfide linkages, are known to be present in long and small TLPs, respectively. These disulfide bonds provide resistance against extreme pH, heat, and protease degradation (<xref ref-type="bibr" rid="B15">Fierens et al., 2009</xref>; <xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>). Each TLP consists of a conserved REDDD motif and a thaumatin signature motif G-X-[GF]-X-C-X-T- [GA]-D-C-X- (1,2)-G-X-(2,3)-C. The REDDD motif is involved in receptor binding for its antifungal action (<xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>). Numerous studies reported that the overexpression of <italic>TLPs</italic> provides significant resistance against various fungi in both dicot and monocot plants (<xref ref-type="bibr" rid="B11">Datta et al., 1999</xref>; <xref ref-type="bibr" rid="B58">Rajam et al., 2007</xref>; <xref ref-type="bibr" rid="B77">Wang et al., 2010</xref>; <xref ref-type="bibr" rid="B10">Cui et al., 2021</xref>). The transgenic <italic>Arabidopsis thaliana</italic> with an overexpressing <italic>PR5</italic> gene (<italic>ObTLP1</italic>) of <italic>Ocimum basilicum</italic> showed enhanced tolerance against <italic>Sclerotinia sclerotiorum</italic> and <italic>Botrytis cinerea</italic> (<xref ref-type="bibr" rid="B46">Misra et al., 2016</xref>). The improved resistance of transgenic wheat against common root rot and leaf rust has been observed in <italic>TaTLP1</italic>-overexpressing transgenic lines (<xref ref-type="bibr" rid="B10">Cui et al., 2021</xref>). The mechanism of action of TLPs in fungal resistance is ambiguous; however, it has been presumed that they work by degradation and permeabilization of the fungal cell walls (<xref ref-type="bibr" rid="B1">Abad et al., 1996</xref>; <xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>). Besides, TLPs are also known to be involved in antifreeze action and abiotic stress resistance in plants (<xref ref-type="bibr" rid="B85">Zhang and Shih, 2007</xref>; <xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>). The overexpression of <italic>GhTLP19</italic> in transgenic <italic>A. thaliana</italic> facilitated the plant with improved resistance against drought stress (<xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>). Further, they are also reported to be involved in various development processes, for instance, flowering, fruit ripening, and seed germination (<xref ref-type="bibr" rid="B50">Neale et al., 1990</xref>; <xref ref-type="bibr" rid="B61">Salzman et al., 1998</xref>; <xref ref-type="bibr" rid="B63">Seo et al., 2008</xref>). Moreover, the upregulation of <italic>TLPs</italic> in response to ethylene, jasmonic acid, and salicylic acid treatment depicted their involvement in the hormonal signaling cascade (<xref ref-type="bibr" rid="B78">Yan et al., 2017</xref>; <xref ref-type="bibr" rid="B37">Li X. et al., 2020</xref>).</p>
<p>Despite utmost importance, a detailed characterization of TLPs is still limited in various cereal crops. Therefore, the current study aims at an inclusive characterization of TLPs in bread wheat, an important cereal crop. Besides, we have also performed a comparative analysis of various features of TLPs in other cereals including <italic>B. distachyon</italic>, <italic>O. sativa</italic>, <italic>S. bicolor</italic>, and <italic>Z. mays</italic>. Chromosomal distribution, phylogeny, physicochemical properties, gene duplication events (DEs), <italic>cis</italic>-regulatory elements, and gene and protein structural analyses were performed. To decipher their roles in plant development and under abiotic and biotic stresses, their expression analysis was performed using high throughput RNA-seq data. The expression of eight selected <italic>TaTLP</italic> genes was validated using qRT-PCR. An abiotic stress-responsive gene, <italic>TaTLP2-B</italic>, of <italic>Triticum aestivum</italic> was cloned and used for functional characterization in <italic>Saccharomyces cerevisiae</italic> (yeast) cells. Recombinant expression of TaTLP2-B provided significant tolerance to the yeast in spot assay against various abiotic stresses. The study will increase the knowledge about numerous TLP proteins and provide the base for the functional characterization of identified genes in future studies.</p>
</sec>
<sec id="S2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="S2.SS1">
<title>Plant Materials, Growth Conditions, and Stress Treatments</title>
<p>Surface sterilization of bread wheat seeds (cv. Chinese Spring) was done with the solution having 1.2% sodium hypochlorite in 10% ethanol. Thereafter, the seeds were washed carefully with the double autoclaved water. The sterilized seeds were kept overnight on moist Whatman filter papers at 4&#x00B0;C for stratification and were further kept at room temperature for germination. The seedlings were then transferred to fresh phytajars and were allowed to grow in plant growth chambers under 60% relative humidity, 22&#x00B0;C temperature, and a 16 and 8 hours (h) light and dark period, respectively (<xref ref-type="bibr" rid="B35">Lei et al., 2021</xref>). For the stress treatments, the 7-days-old seedlings were kept under heat (40&#x00B0;C), osmotic [20% Polyethylene glycol (PEG)], and combined heat and osmotic stress treatments (40&#x00B0;C and 20% PEG) for 6, 12, 24, and 48 h. Similarly, for salinity stress, 7-days-old seedlings were subjected to 150 mM NaCl treatment for 6, 12, 24, and 48 h. However, for the control plants, the seedlings grown in normal conditions were used. The plant samples including roots and shoots were collected at the interval of 6, 12, 24, and 48 h of stress treatments and stored at &#x2013;80&#x00B0;C till further experiments. These stress conditions were selected based on the earlier reports. Further, the RNA seq data of <italic>T. aestivum</italic> used for the <italic>in silico</italic> expression analyses were generated under the same conditions (<xref ref-type="bibr" rid="B42">Liu et al., 2015</xref>; <xref ref-type="bibr" rid="B84">Zhang et al., 2016</xref>).</p>
</sec>
<sec id="S2.SS2">
<title>Identification and Nomenclature of the Thaumatin-Like Protein Genes</title>
<p>Extensive BLAST searches were used to identify the TLP proteins in five different cereals including <italic>B. distachyon</italic>, <italic>O. sativa</italic>, <italic>S. bicolor</italic>, <italic>T. aestivum</italic>, and <italic>Z. mays</italic>. Arabidopsis TLP sequences were used as a query against the protein model sequences of each crop downloaded from the Ensembl Plants (<xref ref-type="bibr" rid="B56">Petre et al., 2011</xref>; <xref ref-type="bibr" rid="B64">Sharma A. et al., 2020</xref>). The presence of the thaumatin (PF00314) domain was analyzed using the Hidden Markov Model (HMM) and Pfam BLAST searches at an <italic>e</italic>-value 10<sup>&#x2013;&#x2013;10</sup>. Identified TLP sequences were further subjected to the NCBI Conserved Domain Database (CDD) BLAST to further confirm the presence of the thaumatin domain. The TLP proteins, having a complete thaumatin family signature, were selected for further analysis. The identified <italic>TLPs</italic> were named as per their sequence of occurrence at various chromosomes in each crop, except <italic>T. aestivum</italic>. The international rules for gene symbolization of <italic>T. aestivum</italic><sup><xref ref-type="fn" rid="footnote1">1</xref></sup> were followed for the nomenclature of <italic>TaTLPs</italic>.</p>
</sec>
<sec id="S2.SS3">
<title>Chromosomal Localization and Duplication Events</title>
<p>Ensembl Plant<sup><xref ref-type="fn" rid="footnote2">2</xref></sup> was used for gathering the chromosomal and sub-genomic location of <italic>TLPs</italic> of all five crops. The homeologous <italic>TLP</italic> genes in <italic>T. aestivum</italic> were identified based on &#x2265; 90% sequence similarity and their occurrence at the related chromosomes. The MapInspect software was used for the graphical representation of <italic>TLP</italic> genes on their respective chromosomes.<sup><xref ref-type="fn" rid="footnote3">3</xref></sup> DEs were identified using a bidirectional blast hit approach with sequence similarity of &#x2265; 80%, while tandem and segmental DEs were segregated based on their distance and occurrence at respective chromosomes as per the previous studies (<xref ref-type="bibr" rid="B68">Shumayla et al., 2019</xref>).</p>
</sec>
<sec id="S2.SS4">
<title>Multiple Sequence Alignments, Phylogeny, and Structural Analysis</title>
<p>The Muscle and Multalin tools were used for the multiple sequence alignments of all the TLP<italic>s</italic> with a known thaumatin protein (P02883.2| THM1_THADA) to find the conserved residues (<xref ref-type="bibr" rid="B8">Corpet, 1988</xref>; <xref ref-type="bibr" rid="B12">Edgar, 2004</xref>). The phylogenetic tree was constructed by the maximum likelihood method with 1,000 bootstraps using the MEGA X software (<xref ref-type="bibr" rid="B33">Kumar et al., 2018</xref>).</p>
</sec>
<sec id="S2.SS5">
<title>Ka/Ks and Tajima&#x2019;s Relativity Test</title>
<p>The alignment of the protein and nucleotide sequences of the paralogous gene pairs was done using the ClustalOmega server.<sup><xref ref-type="fn" rid="footnote4">4</xref></sup> The synonymous substitution per synonymous site (Ks), the non-synonymous substitution per non-synonymous site (Ka), and their ratio (Ka/Ks) were calculated using the PAL2NAL program (<xref ref-type="bibr" rid="B70">Suyama et al., 2006</xref>; <xref ref-type="bibr" rid="B48">Nagaraju et al., 2020</xref>). The calculation of the divergence time of each pair of duplicated genes was done using the formula T = Ks/2r, where T represents the divergence time and r represents the divergence rate. The divergence rate was assumed to be 6.5 &#x00D7; 10<sup>&#x2013;9</sup> for cereals (<xref ref-type="bibr" rid="B19">Gaut et al., 1996</xref>). The Tajima&#x2019;s relativity test was performed to find out the evolutionary rate between paralogous genes (<xref ref-type="bibr" rid="B71">Tajima, 1993</xref>).</p>
</sec>
<sec id="S2.SS6">
<title>Gene Structure Organization</title>
<p>The genomic and coding DNA sequence (CDS) of identified <italic>TLP</italic> genes were used for the analysis of gene structure in terms of exon-intron organization and intron phases using the GSDS 2.0 server as done in earlier studies (<xref ref-type="bibr" rid="B28">Hu et al., 2015</xref>; <xref ref-type="bibr" rid="B65">Sharma H. et al., 2020</xref>).</p>
</sec>
<sec id="S2.SS7">
<title>Physicochemical Properties of the Thaumatin-Like Proteins</title>
<p>Various physicochemical characteristics such as peptide length, MW, and isoelectric point (pI) were analyzed using the ExPasy tool, which were further confirmed from the Ensembl plants and Sequence Manipulation Suite (<xref ref-type="bibr" rid="B69">Stothard, 2000</xref>; <xref ref-type="bibr" rid="B17">Gasteiger et al., 2005</xref>; <xref ref-type="bibr" rid="B51">Nussbaumer et al., 2013</xref>). Tools including CELLO v.2.5, ngLOC, ProtComp9, and WoLF PSORT were used for the prediction of subcellular localization of TLP proteins (<xref ref-type="bibr" rid="B14">Emanuelsson et al., 2000</xref>; <xref ref-type="bibr" rid="B80">Yu et al., 2006</xref>; <xref ref-type="bibr" rid="B27">Horton et al., 2007</xref>; <xref ref-type="bibr" rid="B31">King and Guda, 2007</xref>). Tools such as Phobius and DAS-TMfilter were used for the prediction of transmembrane regions (<xref ref-type="bibr" rid="B9">Cserzo et al., 2004</xref>; <xref ref-type="bibr" rid="B30">K&#x00E4;ll et al., 2004</xref>). The signal peptides were detected using the tools Phobius and SignalP (<xref ref-type="bibr" rid="B30">K&#x00E4;ll et al., 2004</xref>; <xref ref-type="bibr" rid="B55">Petersen et al., 2011</xref>). SMART server was used for the domain analysis, whereas, motifs were analyzed using MEME v.4.11.4 (<xref ref-type="bibr" rid="B4">Bailey et al., 2009</xref>; <xref ref-type="bibr" rid="B36">Letunic et al., 2015</xref>).</p>
</sec>
<sec id="S2.SS8">
<title><italic>Cis</italic>-Regulatory Element Analysis</title>
<p>For <italic>cis</italic>-regulatory elements analysis, 1.5 kb upstream genomic sequences from the initiation codon were retrieved for each <italic>TLP</italic> gene. These promoter sequences were analyzed using the PLACE software (<xref ref-type="bibr" rid="B25">Higo et al., 1998</xref>). The identified <italic>cis</italic>-regulatory elements were categorized based on their functions.</p>
</sec>
<sec id="S2.SS9">
<title>Expression Profiling Using RNA-Seq Data</title>
<p>Expression analysis in various tissues of each crop was done using the high throughput RNA-seq data retrieved from the Unit&#x00E9; de Recherche G&#x00E9;nomique Info (URGI) database<sup><xref ref-type="fn" rid="footnote5">5</xref></sup> and Expression ATLAS (<xref ref-type="bibr" rid="B6">Choulet et al., 2014</xref>; <xref ref-type="bibr" rid="B57">Pingault et al., 2015</xref>; <xref ref-type="bibr" rid="B52">Papatheodorou et al., 2018</xref>). In <italic>T. aestivum</italic>, the expression data generated in replicates for various tissue developmental stages, under biotic (fungal pathogen) and abiotic (heat, osmotic and salt) stress conditions in various studies, were used (<xref ref-type="bibr" rid="B81">Zhang et al., 2014</xref>, <xref ref-type="bibr" rid="B84">2016</xref>; <xref ref-type="bibr" rid="B42">Liu et al., 2015</xref>). Data available for three developmental stages of root, stem, leaf, spike, and grain were used to analyze the tissue-specific expression in wheat. Further, the RNA-seq data (PRJNA243835) available in triplicates after the 24, 48, and 72 h of inoculation of <italic>Blumeria graminis</italic> f. sp. <italic>tritici</italic> (Bgt) and <italic>Puccinia striiformis</italic> f. sp. <italic>tritici</italic> (Pst) in 7-days-old seedlings were used for the <italic>TaTLP</italic> expression analysis under biotic stress (<xref ref-type="bibr" rid="B81">Zhang et al., 2014</xref>). Under abiotic stress conditions, duplicate RNA-seq data (SRP045409) for 1 and 6 h of treatments of heat (40&#x00B0;C), osmotic (20% PEG 6000), and a combination of both heat and osmotic stresses were used to study the <italic>TaTLP</italic> expression (<xref ref-type="bibr" rid="B42">Liu et al., 2015</xref>). Moreover, <xref ref-type="bibr" rid="B42">Liu et al. (2015)</xref> used the term drought stress for PEG treatment, but in the current study, the term osmotic stress has been used for PEG treatment because it actually causes osmotic stress that leads to water stress. Root RNA-seq data (SRP062745) available in triplicates for the treatment of 150 mM NaCl at 6, 12, 24, and 48 h were used to analyze the expression of <italic>TaTLPs</italic> under salt stress (<xref ref-type="bibr" rid="B84">Zhang et al., 2016</xref>). Trinity package was used to calculate the expression value in terms of fragments per kilobase of exon per million mapped fragments (FPKM) value (<xref ref-type="bibr" rid="B22">Haas et al., 2013</xref>). Hierarchical Clustering Explorer 3.5 was used to generate heat maps of differentially expressed genes, which were clustered using the Euclidean distance method (<xref ref-type="bibr" rid="B62">Seo et al., 2006</xref>).</p>
</sec>
<sec id="S2.SS10">
<title>RNA Isolation, cDNA Synthesis, and qRT-PCR</title>
<p>The 7-days-old seedlings treated with various abiotic stresses were harvested after the 6, 12, 24, and 48 h of stress treatments. The root and shoot tissues of these seedlings were used for the total RNA isolation. The total RNA of each sample was isolated using the Spectrum&#x2122; Plant Total RNA kit (Sigma, United States). The seedlings (shoot and root) grown under normal conditions were used as a control. The TURBO DNA-free &#x2122; Kit (Invitrogen, United States) was used to remove the genomic DNA contamination. The qualitative and quantitative analysis of RNA were done using agarose gel electrophoresis and NanoDrop quantification, respectively. The Superscript III First-Strand Synthesis Super-mix (Invitrogen, United States) was used to synthesize the cDNA from one microgram of total RNA. A real-time qRT-PCR was performed with the gene-specific primers of selected genes using SYBR Green at the 7900 HT Fast Real-Time PCR System (Applied Biosystems) following the method established in our laboratory (<xref ref-type="bibr" rid="B68">Shumayla et al., 2019</xref>). The fold expression change was calculated using the delta-delta CT method (2<sup>&#x2013;&#x0394;&#x0394;<italic>CT</italic></sup>) using the expression of ADP-ribosylation factor (<italic>TaARF</italic>) as an internal control as reported in earlier studies (<xref ref-type="bibr" rid="B43">Livak and Schmittgen, 2001</xref>; <xref ref-type="bibr" rid="B68">Shumayla et al., 2019</xref>; <xref ref-type="bibr" rid="B72">Tyagi et al., 2021</xref>). All the experiments were carried out in three biological replicates and expressed as mean &#x00B1; SD. A significant difference between the control and treatments was examined by using the two-tailed student&#x2019;s <italic>t</italic>-test.</p>
</sec>
<sec id="S2.SS11">
<title>Cloning and Functional Characterization</title>
<p>The full-length open reading frame (ORF) of the <italic>TaTLP2-B</italic> gene was amplified from cDNA using the <italic>TaTLP2-B</italic> forward (5&#x2032; GTAATGGCTCTTCTTCCTCCTCTGCTTCTG 3&#x2032;) and <italic>TaTLP2-B</italic> reverse (5&#x2032; AATCTGGGCCACACGATCGCCCC 3&#x2032;) primers. The amplified DNA was cloned into the pJET1.2 cloning vector and sequenced. <italic>TaTLP2-B</italic> gene was re-amplified from the confirmed clone using the same primers and ligated into the pYES2.1/V5-His-Topo vector (Invitrogen, United States). The recombinant plasmid (pYES2.1-<italic>TaTLP2-B</italic>) was transformed in <italic>S. cerevisiae</italic> (W303) (yeast) cells for further characterization. For control, <italic>lacz</italic> gene containing pYES2.1 vector (pYES2.1/V5-His/lacZ) was used during the studies. Spot assays using recombinant yeast cells were performed under various abiotic stress conditions. Recombinant yeast cells were grown overnight in SD/-ura (with 2% dextrose) medium at 30&#x00B0;C and 200 rpm as primary culture and further inoculated for secondary culture (1:100 dilutions). As soon as OD<sub>600</sub> reached 0.4, 2%, galactose was added to induce the expression of recombinant protein in yeast and kept at 30&#x00B0;C and 200 rpm for 6 h. The OD<sub>600</sub> was adjusted to 0.4 and an equal volume (500 &#x03BC;l) of each induced culture was further diluted in 10 ml medium. The diluted cultures were treated with heat (37 and 40&#x00B0;C), cold (4&#x00B0;C), osmotic (20 and 30% PEG), combined heat and osmotic (37&#x00B0;C, and 30% PEG), and salt (1 M NaCl) stresses for 24 h, separately. After the treatments, serial dilutions (10<sup>0</sup>, 10<sup>&#x2013;2</sup>, 10<sup>&#x2013;4</sup>, and 10<sup>&#x2013;6</sup>) were prepared, 5 &#x03BC;l of each dilution was spotted on SD/-ura agar plates, and incubated at 30&#x00B0;C for 2&#x2013;3 days as reported in earlier studies (<xref ref-type="bibr" rid="B68">Shumayla et al., 2019</xref>). All the experiments were performed in triplicates and the results were compared visually.</p>
</sec>
<sec id="S2.SS12">
<title>Subcellular Localization of the TaTLP2-B</title>
<p>Subcellular localization of TaTLP2-B protein was analyzed using CaMV35S-driven C-terminal yellow fluorescent protein (YFP) fusion construct generated by Gateway LR-recombination into binary vector PEG101. Plasmids were then transformed into <italic>Agrobacterium tumefaciens</italic> GV3101 strain. The cells were resuspended in a freshly prepared infiltration medium (10 mM MgCl<sub>2</sub>, 10 mM MES/KOH, pH 5.7 and 150 &#x03BC;M acetosyringone). The resulting constructs were infiltrated onto the abaxial surface of <italic>Nicotiana benthamiana</italic> leaf and kept at 22&#x00B0;C for 48 h. The YFP fluorescence was observed using the Leica TCS SP8 (Leica Microsystems, Wetzlar, Germany) laser-scanning confocal microscope at 514&#x2013;527 nm.</p>
</sec>
</sec>
<sec id="S3" sec-type="results">
<title>Results</title>
<sec id="S3.SS1">
<title>Identification and Chromosomal Localization of the Thaumatin-Like Protein Genes</title>
<p>Numerous properties of TLPs ascribed to defense and development pathways and lack of such studies in numerous cereals lead us to perform a comprehensive analysis of the TLP family in five major cereals. An extensive BLAST search identified 26, 27, 39, 93, and 37 <italic>TLP</italic> genes in <italic>B</italic>. <italic>distachyon, O</italic>. <italic>sativa, S</italic>. <italic>bicolor, T</italic>. <italic>aestivum</italic>, and <italic>Z</italic>. <italic>mays</italic>, respectively. The genes lacking or having incomplete thaumatin signature motifs were excluded from the study. Four <italic>TLPs</italic> were identified as small <italic>TLPs</italic> (sTLPs) in each <italic>B. distachyon, O. sativa</italic>, and <italic>Z. mays</italic>, while 10 and 20 <italic>sTLPs</italic> were detected in <italic>S. bicolor</italic> and <italic>T. aestivum</italic>, respectively (<xref ref-type="supplementary-material" rid="FS1">Supplementary File 1</xref>). In the case of <italic>T. aestivum</italic>, the identified <italic>TLP</italic> genes from the A, B, and D sub-genomes formed 32 homeologous groups based on their sequence homology (&#x2265;90%). All of the identified proteins exhibited a complete thaumatin signature motif (<xref ref-type="supplementary-material" rid="FS1">Supplementary Figure 1</xref>).</p>
<p>The chromosomal localization suggested the scattered distribution of the <italic>TLP</italic> genes at the majority of chromosomes in each crop (<xref ref-type="fig" rid="F1">Figure 1</xref>). In <italic>B. distachyon</italic>, chromosome 4 consisted of a maximum of 10 <italic>TLP</italic> (both long and small) genes, while in the case of <italic>O. sativa, S. bicolor, T. aestivum</italic>, and <italic>Z. mays</italic>, the majority of genes (6, 11, 18, and 11) were localized on chromosomes 12, 8, 5A, and 1, respectively.</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption><p>Chromosomal distribution and paralogous gene analysis of Thaumatin-like proteins <italic>(TLPs)</italic> in five cereal crops. Image depicts the scattered localization of <italic>TLP</italic> genes of <bold>(A)</bold> <italic>B. distachyon</italic>, <bold>(B)</bold> <italic>O. sativa</italic>, <bold>(C)</bold> <italic>S. bicolor</italic>, <bold>(D)</bold> <italic>T. aestivum</italic>, and <bold>(E)</bold> <italic>Z. mays</italic> at their respective chromosomes. Red lines and blue lines denote the tandem and segmental duplication events, respectively.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-12-807448-g001.tif"/>
</fig>
</sec>
<sec id="S3.SS2">
<title>Multiple Sequence Alignments</title>
<p>Thaumatin-like proteins consist of various characteristic and conserved residues, which are important for their functional activities. Multiple sequence alignments of TLP proteins with a known thaumatin protein (P02883.2| THM1_THADA) revealed the identification of 16 and 10 conserved cysteine residues in the majority of long and small TLP proteins of the studied cereal crops, respectively. Moreover, 7&#x2013;15 cysteine residues had also been observed in a few TLPs of <italic>O. sativa, S. bicolor, T. aestivum</italic>, and <italic>Z. mays</italic>. The REDDD motif was also found conserved in the majority of TLP proteins. However, in certain TLP proteins, a few amino acid residues (AAs) were replaced by other AAs having either similar or different properties. For instance, Arginine (R) was replaced by Lysine (K) or Asparagine (N). This could be responsible for the differential evolvement of various characteristic features of TLPs during evolution. The thaumatin signature motif, which is a characteristic feature of TLPs (<xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>), was found to be highly conserved in all the identified TLP proteins. Some other regions like FF hydrophobic motif and bottom of acidic cleft forming amino acids were also found to be well conserved (<xref ref-type="fig" rid="F2">Figure 2</xref> and <xref ref-type="supplementary-material" rid="FS1">Supplementary Figure 1</xref>).</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption><p>Multiple sequence alignment of selected long and small TLPs of <italic>B. distachyon, O. sativa, S. bicolor, T. aestivum</italic>, and <italic>Z. mays</italic> with a known thaumatin protein sequence. Figure shows the alignment of long (OsTLP5, SbTLP2, BdTLP13, ZmTLP13, and TaTLP1-A) and small (BdTLP10, OsTLP25, ZmTLP6, SbTLP29, and TaTLP6-B) TLPs with a known thaumatin (P02883.2| THM1_THADA) protein sequence. The characteristic thaumatin signature motif is shown in the sky blue box. All the conserved cysteine residues were marked with an asterisk. The REDDD motif was marked with a red circle. The FF hydrophobic motif and bottom of acidic cleft forming regions are marked with a green triangle and brown box, respectively. The conserved regions of the thaumatin domain are marked with a black line.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-12-807448-g002.tif"/>
</fig>
</sec>
<sec id="S3.SS3">
<title>Evolutionary Analyses</title>
<sec id="S3.SS3.SSS1">
<title>Phylogeny</title>
<p>To decipher the evolutionary relationship, a phylogenetic tree was built using the full-length TLP protein sequences of the five cereals and <italic>A. thaliana</italic>. These were clustered into 11 different clades based on their phylogenetic relatedness, named as groups I&#x2013;XI (<xref ref-type="fig" rid="F3">Figure 3</xref>). The highest number of TLPs was found in group XI, followed by group II and group X, while group IV was the smallest with only five genes. All the sTLPs were tightly clustered into group XI, which could be due to their smaller size. Further, the majority of groups consisted of TLPs from all the five cereals, except groups III, V, and VI that lacked members from one or more plant species. Besides, group IV comprised only three TaTLP and two AtTLP proteins. Besides, the homeologous TaTLPs of <italic>T. aestivum</italic> were tightly clustered in proximity.</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption><p>Phylogenetic tree analysis of <italic>A. thaliana, B. distachyon, O. sativa. S, bicolor, T. aestivum, and Z. mays</italic> using full-length peptide of TLPs. The figure shows the phylogenetic tree of TLPs, built by the maximum likelihood approach with 1000 bootstrap values using MEGA X software. The phylogenetic tree displays the clustering of TLPs of six plant species in I-XI different groups, each group is colored differently. The TLPs from each plant are marked with a different color.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-12-807448-g003.tif"/>
</fig>
</sec>
<sec id="S3.SS3.SSS2">
<title>Duplication Events Investigation</title>
<p>Duplication event analyses were carried out to understand their roles in the evolution and expansion of the TLP gene family in the studied crop species. A total of one, four, three, six, and eight DEs were predicted in <italic>B. distachyon, O. sativa, S. bicolor</italic>, <italic>T. aestivum</italic>, and <italic>Z mays</italic>, respectively (<xref ref-type="fig" rid="F1">Figure 1</xref> and <xref ref-type="supplementary-material" rid="FS1">Supplementary File 2</xref>). Only tandem DEs (TDEs) were found in the case of paralogous genes of <italic>B. distachyon</italic> (<italic>BdTLP1-BdTLP2</italic>), <italic>O. sativa</italic> (<italic>OsTLP5-OsTLP7, OsTLP22-OsTLP24</italic>, etc.), and <italic>S. bicolor</italic> (<italic>SbTLP28-SbTLP29, SbTLP31-SbTLP34</italic>, etc.). However, in the case of <italic>T. aestivum</italic>, five DEs (<italic>TaTLP1-A-TaTLP24-D, TaTLP1-B-TaTLP24-B</italic>, etc.) were segmental and one was TDE (<italic>TaTLP16-A-TaTLP17-A</italic>). In <italic>Z. mays</italic>, seven segmental (<italic>ZmTLP1-ZmTLP35, ZmTLP2-ZmTLP34</italic>, etc.) and one TDE (<italic>ZmTLP6-ZmTLP7</italic>) were found. All the duplicated gene pairs of each cereal crop were tightly clustered in proximity in the phylogenetic tree.</p>
</sec>
<sec id="S3.SS3.SSS3">
<title>Ka/Ks and Tajima&#x2019;s Relative Rate Test</title>
<p>Over the course of evolution, various evolutionary forces and natural pressures affected the duplicated genes (<xref ref-type="bibr" rid="B13">Ellegren, 2008</xref>). To understand the evolutionary divergence between the paralogous gene pairs, the Ka/Ks analysis was carried out. The Ka/Ks ratio of more than one suggests the positive (non-purifying) and less than one indicates negative (purifying) selection pressure. All the paralogous genes showed the Ka/Ks value lesser than one, which suggested the negative or purifying selection on duplicated <italic>TLP</italic> genes (<xref ref-type="table" rid="T1">Table 1</xref>). However, Ka/Ks analysis for <italic>ZmTLP6</italic> and <italic>ZmTLP7</italic> was not performed due to their 100% similarity. Additionally, the divergence time of DEs was also calculated using the Ks value and previously described methods (<xref ref-type="bibr" rid="B29">Huang et al., 2002</xref>; <xref ref-type="bibr" rid="B66">Sharma et al., 2014</xref>). The divergence time of duplicated genes was calculated as 83 million years ago (MYA) in <italic>BdTLPs</italic>, while the range varied from 52 to 108, 6 to 137, 63 to 99, and 1 to 63 MYA in <italic>O. sativa, S. bicolor, T. aestivum</italic> and <italic>Z. mays</italic>, respectively (<xref ref-type="table" rid="T1">Table 1</xref>). Tajima&#x2019;s relative rate test found the insignificant &#x03C7;<sup>2</sup>-value for all the duplicated gene pairs at <italic>P</italic> &#x003E; 0.05 (<xref ref-type="table" rid="T2">Table 2</xref>). The <italic>P</italic>-value of more than 0.05 depicted their acceptance of the molecular evolutionary clock hypothesis (<xref ref-type="bibr" rid="B71">Tajima, 1993</xref>).</p>
<table-wrap position="float" id="T1">
<label>TABLE 1</label>
<caption><p>The Ka/Ks ratio and divergence time of duplicated <italic>TLP</italic> gene pairs.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Gene A</td>
<td valign="top" align="center">Gene B</td>
<td valign="top" align="center">Ka</td>
<td valign="top" align="center">Ks</td>
<td valign="top" align="center">Ka/Ks</td>
<td valign="top" align="center">Selection pressure</td>
<td valign="top" align="center">T = Ks/2r</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><italic>BdTLPK1</italic></td>
<td valign="top" align="center"><italic>BdTLPK2</italic></td>
<td valign="top" align="center">0.1102</td>
<td valign="top" align="center">1.0810</td>
<td valign="top" align="center">0.1020</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">83.2</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP5</italic></td>
<td valign="top" align="center"><italic>OsTLP7</italic></td>
<td valign="top" align="center">0.1014</td>
<td valign="top" align="center">0.6788</td>
<td valign="top" align="center">0.1494</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">52.2</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP22</italic></td>
<td valign="top" align="center"><italic>OsTLP24</italic></td>
<td valign="top" align="center">0.0697</td>
<td valign="top" align="center">0.4134</td>
<td valign="top" align="center">0.3190</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">27.7</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP23</italic></td>
<td valign="top" align="center"><italic>OsTLP25</italic></td>
<td valign="top" align="center">0.1149</td>
<td valign="top" align="center">0.3603</td>
<td valign="top" align="center">0.31646</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">29.4</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP26</italic></td>
<td valign="top" align="center"><italic>OsTLP27</italic></td>
<td valign="top" align="center">0.1569</td>
<td valign="top" align="center">1.3980</td>
<td valign="top" align="center">0.1122</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">107.6</td>
</tr>
<tr>
<td valign="top" align="left"><italic>SbTLP28</italic></td>
<td valign="top" align="center"><italic>SbTLP29</italic></td>
<td valign="top" align="center">0.0911</td>
<td valign="top" align="center">0.6808</td>
<td valign="top" align="center">0.1338</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">52.4</td>
</tr>
<tr>
<td valign="top" align="left"><italic>SbTLP31</italic></td>
<td valign="top" align="center"><italic>SbTLP34</italic></td>
<td valign="top" align="center">0.1388</td>
<td valign="top" align="center">1.7816</td>
<td valign="top" align="center">0.0779</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">137</td>
</tr>
<tr>
<td valign="top" align="left"><italic>SbTLP32</italic></td>
<td valign="top" align="center"><italic>SbTLP33</italic></td>
<td valign="top" align="center">0.0055</td>
<td valign="top" align="center">0.0716</td>
<td valign="top" align="center">0.0771</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">5.5</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP1-A</italic></td>
<td valign="top" align="center"><italic>TaTLP24-D</italic></td>
<td valign="top" align="center">0.1224</td>
<td valign="top" align="center">0.8739</td>
<td valign="top" align="center">0.1401</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">67.2</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP1-B</italic></td>
<td valign="top" align="center"><italic>TaTLP24-B</italic></td>
<td valign="top" align="center">0.0937</td>
<td valign="top" align="center">0.8163</td>
<td valign="top" align="center">0.1148</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">62.8</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP12-B</italic></td>
<td valign="top" align="center"><italic>TaTLP13-D</italic></td>
<td valign="top" align="center">0.1193</td>
<td valign="top" align="center">1.1836</td>
<td valign="top" align="center">0.1008</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">91</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP15-A</italic></td>
<td valign="top" align="center"><italic>TaTLP18-B</italic></td>
<td valign="top" align="center">0.1368</td>
<td valign="top" align="center">0.9879</td>
<td valign="top" align="center">0.1384</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">76</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP15-B2</italic></td>
<td valign="top" align="center"><italic>TaTLP18-A</italic></td>
<td valign="top" align="center">0.1423</td>
<td valign="top" align="center">0.9582</td>
<td valign="top" align="center">0.1486</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">73.7</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP16-A</italic></td>
<td valign="top" align="center"><italic>TaTLP17-A</italic></td>
<td valign="top" align="center">0.1456</td>
<td valign="top" align="center">1.2825</td>
<td valign="top" align="center">0.1135</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">98.7</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP1</italic></td>
<td valign="top" align="center"><italic>ZmTLP35</italic></td>
<td valign="top" align="center">0.0955</td>
<td valign="top" align="center">0.3929</td>
<td valign="top" align="center">0.2431</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">30.2</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP2</italic></td>
<td valign="top" align="center"><italic>ZmTLP34</italic></td>
<td valign="top" align="center">0.1044</td>
<td valign="top" align="center">0.8149</td>
<td valign="top" align="center">0.1281</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">62.7</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP3</italic></td>
<td valign="top" align="center"><italic>ZmTLP22</italic></td>
<td valign="top" align="center">0.0495</td>
<td valign="top" align="center">0.3036</td>
<td valign="top" align="center">0.1630</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">23.4</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP9</italic></td>
<td valign="top" align="center"><italic>ZmTLP12</italic></td>
<td valign="top" align="center">0.0767</td>
<td valign="top" align="center">0.3783</td>
<td valign="top" align="center">0.2027</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">29.1</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP13</italic></td>
<td valign="top" align="center"><italic>ZmTLP37</italic></td>
<td valign="top" align="center">0.0523</td>
<td valign="top" align="center">0.3200</td>
<td valign="top" align="center">0.1634</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">24.7</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP16</italic></td>
<td valign="top" align="center"><italic>ZmTLP33</italic></td>
<td valign="top" align="center">0.0133</td>
<td valign="top" align="center">0.0141</td>
<td valign="top" align="center">0.9483</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">1.1</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP20</italic></td>
<td valign="top" align="center"><italic>ZmTLP25</italic></td>
<td valign="top" align="center">0.0797</td>
<td valign="top" align="center">0.0889</td>
<td valign="top" align="center">0.8965</td>
<td valign="top" align="center">Purifying</td>
<td valign="top" align="center">6.9</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn><p><italic>Ka, non-synonymous substitutions per non-synonymous site; Ks, synonymous substitutions per synonymous site; T, Divergence time.</italic></p></fn>
</table-wrap-foot>
</table-wrap>
<table-wrap position="float" id="T2">
<label>TABLE 2</label>
<caption><p>Tajima&#x2019;s relative rate test of paralogous genes.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Group A</td>
<td valign="top" align="center">Group B</td>
<td valign="top" align="center">Outgroup</td>
<td valign="top" align="center">Nt</td>
<td valign="top" align="center">Na</td>
<td valign="top" align="center">Nb</td>
<td valign="top" align="center">&#x03C7;<sup>2</sup></td>
<td valign="top" align="center"><italic>P</italic></td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><italic>BdTLP1</italic></td>
<td valign="top" align="center"><italic>BdTLP2</italic></td>
<td valign="top" align="center"><italic>BdTLP11</italic></td>
<td valign="top" align="center">403</td>
<td valign="top" align="center">47</td>
<td valign="top" align="center">42</td>
<td valign="top" align="center">0.28</td>
<td valign="top" align="center">0.59611</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP5</italic></td>
<td valign="top" align="center"><italic>OsTLP7</italic></td>
<td valign="top" align="center"><italic>OsTLP18</italic></td>
<td valign="top" align="center">401</td>
<td valign="top" align="center">28</td>
<td valign="top" align="center">29</td>
<td valign="top" align="center">0.02</td>
<td valign="top" align="center">0.89463</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP22</italic></td>
<td valign="top" align="center"><italic>OsTLP24</italic></td>
<td valign="top" align="center"><italic>OsTLP18</italic></td>
<td valign="top" align="center">333</td>
<td valign="top" align="center">15</td>
<td valign="top" align="center">17</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.72367</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP23</italic></td>
<td valign="top" align="center"><italic>OsTLP25</italic></td>
<td valign="top" align="center"><italic>OsTLP18</italic></td>
<td valign="top" align="center">313</td>
<td valign="top" align="center">20</td>
<td valign="top" align="center">27</td>
<td valign="top" align="center">1.04</td>
<td valign="top" align="center">0.30723</td>
</tr>
<tr>
<td valign="top" align="left"><italic>OsTLP26</italic></td>
<td valign="top" align="center"><italic>OsTLP27</italic></td>
<td valign="top" align="center"><italic>OsTLP18</italic></td>
<td valign="top" align="center">411</td>
<td valign="top" align="center">34</td>
<td valign="top" align="center">34</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td valign="top" align="left"><italic>SbTLP28</italic></td>
<td valign="top" align="center"><italic>SbTLP29</italic></td>
<td valign="top" align="center"><italic>SbTLP5</italic></td>
<td valign="top" align="center">316</td>
<td valign="top" align="center">19</td>
<td valign="top" align="center">30</td>
<td valign="top" align="center">2.47</td>
<td valign="top" align="center">0.11608</td>
</tr>
<tr>
<td valign="top" align="left"><italic>SbTLP31</italic></td>
<td valign="top" align="center"><italic>SbTLP34</italic></td>
<td valign="top" align="center"><italic>SbTLP5</italic></td>
<td valign="top" align="center">312</td>
<td valign="top" align="center">27</td>
<td valign="top" align="center">32</td>
<td valign="top" align="center">0.42</td>
<td valign="top" align="center">0.51508</td>
</tr>
<tr>
<td valign="top" align="left"><italic>SbTLP32</italic></td>
<td valign="top" align="center"><italic>SbTLP33</italic></td>
<td valign="top" align="center"><italic>SbTLP5</italic></td>
<td valign="top" align="center">347</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP1-A</italic></td>
<td valign="top" align="center"><italic>TaTLP24-D</italic></td>
<td valign="top" align="center"><italic>TaTLP4-D</italic></td>
<td valign="top" align="center">483</td>
<td valign="top" align="center">37</td>
<td valign="top" align="center">30</td>
<td valign="top" align="center">0.73</td>
<td valign="top" align="center">0.39245</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP1-B</italic></td>
<td valign="top" align="center"><italic>TaTLP24-B</italic></td>
<td valign="top" align="center"><italic>TaTLP4-D</italic></td>
<td valign="top" align="center">486</td>
<td valign="top" align="center">36</td>
<td valign="top" align="center">31</td>
<td valign="top" align="center">0.37</td>
<td valign="top" align="center">0.5413</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP12-B</italic></td>
<td valign="top" align="center"><italic>TaTLP13-D</italic></td>
<td valign="top" align="center"><italic>TaTLP4-D</italic></td>
<td valign="top" align="center">321</td>
<td valign="top" align="center">24</td>
<td valign="top" align="center">33</td>
<td valign="top" align="center">1.42</td>
<td valign="top" align="center">0.23323</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP15-A</italic></td>
<td valign="top" align="center"><italic>TaTLP18-B</italic></td>
<td valign="top" align="center"><italic>TaTLP4-D</italic></td>
<td valign="top" align="center">391</td>
<td valign="top" align="center">36</td>
<td valign="top" align="center">38</td>
<td valign="top" align="center">0.05</td>
<td valign="top" align="center">0.81615</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP15-B2</italic></td>
<td valign="top" align="center"><italic>TaTLP18-A</italic></td>
<td valign="top" align="center"><italic>TaTLP4-D</italic></td>
<td valign="top" align="center">260</td>
<td valign="top" align="center">28</td>
<td valign="top" align="center">27</td>
<td valign="top" align="center">0.02</td>
<td valign="top" align="center">0.89274</td>
</tr>
<tr>
<td valign="top" align="left"><italic>TaTLP16-A</italic></td>
<td valign="top" align="center"><italic>TaTLP17-A</italic></td>
<td valign="top" align="center"><italic>TaTLP4-D</italic></td>
<td valign="top" align="center">291</td>
<td valign="top" align="center">36</td>
<td valign="top" align="center">31</td>
<td valign="top" align="center">0.37</td>
<td valign="top" align="center">0.5413</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP1</italic></td>
<td valign="top" align="center"><italic>ZmTLP35</italic></td>
<td valign="top" align="center"><italic>ZmTLP28</italic></td>
<td valign="top" align="center">551</td>
<td valign="top" align="center">36</td>
<td valign="top" align="center">33</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.71798</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP2</italic></td>
<td valign="top" align="center"><italic>ZmTLP34</italic></td>
<td valign="top" align="center"><italic>ZmTLP28</italic></td>
<td valign="top" align="center">541</td>
<td valign="top" align="center">34</td>
<td valign="top" align="center">25</td>
<td valign="top" align="center">1.37</td>
<td valign="top" align="center">0.24132</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP3</italic></td>
<td valign="top" align="center"><italic>ZmTLP22</italic></td>
<td valign="top" align="center"><italic>ZmTLP28</italic></td>
<td valign="top" align="center">560</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">14</td>
<td valign="top" align="center">0.36</td>
<td valign="top" align="center">0.54851</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP9</italic></td>
<td valign="top" align="center"><italic>ZmTLP12</italic></td>
<td valign="top" align="center"><italic>ZmTLP28</italic></td>
<td valign="top" align="center">372</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0.1573</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP13</italic></td>
<td valign="top" align="center"><italic>ZmTLP37</italic></td>
<td valign="top" align="center"><italic>ZmTLP28</italic></td>
<td valign="top" align="center">464</td>
<td valign="top" align="center">19</td>
<td valign="top" align="center">22</td>
<td valign="top" align="center">0.22</td>
<td valign="top" align="center">0.63941</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP16</italic></td>
<td valign="top" align="center"><italic>ZmTLP33</italic></td>
<td valign="top" align="center"><italic>ZmTLP28</italic></td>
<td valign="top" align="center">551</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">0.33</td>
<td valign="top" align="center">0.5637</td>
</tr>
<tr>
<td valign="top" align="left"><italic>ZmTLP20</italic></td>
<td valign="top" align="center"><italic>ZmTLP25</italic></td>
<td valign="top" align="center"><italic>ZmTLP28</italic></td>
<td valign="top" align="center">525</td>
<td valign="top" align="center">17</td>
<td valign="top" align="center">23</td>
<td valign="top" align="center">0.9</td>
<td valign="top" align="center">0.34278</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn><p><italic>Nt, Identical sites in all three sequences; Na, Unique differences in Sequence A; Nb, Unique differences in Sequence B.</italic></p></fn>
</table-wrap-foot>
</table-wrap>
</sec>
</sec>
<sec id="S3.SS4">
<title>Gene Architecture, Domain, and Motif Analyses</title>
<p>The number of exons varied from one to three in <italic>O. sativa</italic>, while one to four in <italic>B. distachyon, S. bicolor</italic>, and <italic>T. aestivum</italic>. In the case of <italic>Z. mays</italic>, most of the <italic>TLPs</italic> consisted of one to three exons, while <italic>ZmTLP16, ZmTLP20, ZmTLP25</italic>, and <italic>ZmTLP33</italic> exhibited eleven, seven, eight, and ten exons, respectively. Moreover, a total of 44% (98/222) identified <italic>TLPs</italic> were intronless. Intriguingly, all the <italic>sTLPs</italic> were intronless, except <italic>TaTLP6-A</italic> and <italic>TaTLP20-A1</italic>. The intron phase analysis revealed that the occurrence of a maximum number of introns in phase 1, followed by phase 2, while the least number of introns were in phase 0 (<xref ref-type="supplementary-material" rid="FS2">Supplementary Figure 2</xref>).</p>
<p>The functional nature of a protein depends upon the occurrence of domain composition. All of the identified cereals&#x2019; TLPs consisted of a thaumatin domain (PF00314), which confirmed that they are TLPs. The size of the thaumatin domain ranged from 202&#x2013;217 AAs to 134&#x2013;154 AAs in the long and small TLPs, respectively. In addition to the thaumatin domain, ZmTLP16, ZmTLP20, ZmTLP25, and ZmTLP33 also consisted of a nuclear protein 96 (NUP96) domain of &#x223C;211 AAs at the C-terminus of these proteins (<xref ref-type="supplementary-material" rid="FS1">Supplementary File 3</xref>).</p>
<p>Motif investigation revealed the occurrence of 10 highly conserved motifs in the TLP proteins. Motifs 1&#x2013;9 were parts of the thaumatin domain, while motif 10 was unknown. Motifs 5, 6, and 8 were the most conserved motifs in TLP proteins, in which the thaumatin signature sequence was present in motif 8 (<xref ref-type="supplementary-material" rid="FS2">Supplementary Figure 2</xref>). The occurrence of conserved motifs across the cereal species suggested the conserved nature of TLP proteins in related plant species.</p>
</sec>
<sec id="S3.SS5">
<title>Physicochemical Properties</title>
<p>To understand the various important features, several physicochemical properties of identified TLPs were studied. The TLPs were analyzed for MW, peptide length, isoelectric point (pI), subcellular localization, transmembrane (TM) helix, and signal peptide (<xref ref-type="supplementary-material" rid="FS1">Supplementary File 4</xref>). The average length of the long and small TLPs ranged from 284&#x2013;334 AAs to 175&#x2013;185 AAs in the studied cereal crops, respectively. Similarly, the average MWs ranged from &#x223C;29&#x2013;35 kDa to &#x223C;17&#x2013;19 kDa, respectively. However, the average pI ranged from 5.89 to 6.95 and from 4.90 to 6.82 for the long and small TLPs, respectively (<xref ref-type="table" rid="T3">Table 3</xref> and <xref ref-type="supplementary-material" rid="FS1">Supplementary File 4</xref>).</p>
<table-wrap position="float" id="T3">
<label>TABLE 3</label>
<caption><p>Physicochemical properties of long and small TLP proteins.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Property</td>
<td valign="top" align="left">Type</td>
<td valign="top" align="left"><italic>Brachypodium distachyon</italic></td>
<td valign="top" align="left"><italic>Oryza sativa</italic></td>
<td valign="top" align="left"><italic>Sorghum bicolor</italic></td>
<td valign="top" align="left"><italic>Triticum aestivum</italic></td>
<td valign="top" align="center"><italic>Zea mays</italic></td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><bold>Average protein length</bold></td>
<td valign="top" align="left">Long TLPs</td>
<td valign="top" align="left">299</td>
<td valign="top" align="left">289</td>
<td valign="top" align="left">294</td>
<td valign="top" align="left">284</td>
<td valign="top" align="center">334</td>
</tr>
<tr>
<td/>
<td valign="top" align="left">Small TLPs</td>
<td valign="top" align="left">185</td>
<td valign="top" align="left">178</td>
<td valign="top" align="left">178</td>
<td valign="top" align="left">177</td>
<td valign="top" align="center">175</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Average molecular weight (kDa)</bold></td>
<td valign="top" align="left">Long TLPs</td>
<td valign="top" align="left">30.8</td>
<td valign="top" align="left">29.8</td>
<td valign="top" align="left">30.0</td>
<td valign="top" align="left">29.1</td>
<td valign="top" align="center">35.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left">Small TLPs</td>
<td valign="top" align="left">19.5</td>
<td valign="top" align="left">18.1</td>
<td valign="top" align="left">18.3</td>
<td valign="top" align="left">18.22</td>
<td valign="top" align="center">17.7</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Average pI</bold></td>
<td valign="top" align="left">Long TLPs</td>
<td valign="top" align="left">6.18</td>
<td valign="top" align="left">6.95</td>
<td valign="top" align="left">6.05</td>
<td valign="top" align="left">6.18</td>
<td valign="top" align="center">5.89</td>
</tr>
<tr>
<td/>
<td valign="top" align="left">Small TLPs</td>
<td valign="top" align="left">6.82</td>
<td valign="top" align="left">6.06</td>
<td valign="top" align="left">5.74</td>
<td valign="top" align="left">6.17</td>
<td valign="top" align="center">4.90</td>
</tr>
</tbody>
</table></table-wrap>
<p>The majority of TLP proteins lacked TM helices, which suggested their soluble/cytoplasmic nature. However, five TLPs of <italic>B. distachyon</italic> and <italic>O. sativa</italic>, seven of <italic>T. aestivum</italic> and <italic>Z. mays</italic>, and 10 TLPs of <italic>S. bicolor</italic> consisted of a single TM region, and OsTLP18, TaTLP4-D, and TaTLP5-D comprised of two TM helices, which suggested their membrane-bound nature (<xref ref-type="supplementary-material" rid="FS1">Supplementary File 4</xref>).</p>
<p>A total of 23, 21, 36, 86, and 33 TLPs of <italic>B. distachyon, O. sativa, S. bicolor</italic>, <italic>T. aestivum</italic>, and <italic>Z. mays</italic> consisted of the N-terminal signal peptide, respectively. Further, the majority of TLP proteins were predicted to be localized in the extracellular region, while three TLPs from <italic>O. sativa</italic> (OsTLP10, OsTLP15 and OsTLP16) showed nuclear, and BdTLP16, TaTLP21-A, ZmTLP20, ZmTLP25, and ZmTLP33 showed plasma membrane localization (<xref ref-type="supplementary-material" rid="FS1">Supplementary File 4</xref>). To validate the subcellular localization, a <italic>TLP</italic> gene (<italic>TaTLP2-B</italic>) was cloned and expressed with YFP as a translational fusion protein. Analysis of YFP fluorescence of fusion protein confirmed its extracellular localization (<xref ref-type="fig" rid="F4">Figure 4</xref>). Moreover, we could also see some fluorescence in the cytoplasmic region. The results suggested that the majority of TaTLP2-B was localized in the extracellular region, where it could be involved in various defense-related functions (such as anti-fungal etc.). The cytoplasmic localization could be due to its translation in the cytoplasm, or it might also function inside the cytoplasm.</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption><p>Subcellular localization analysis of TaTLP2-B by YFP fusion. The YFP fluorescence depicts the localization of TaTLP2-B protein majorly in the extracellular region.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-12-807448-g004.tif"/>
</fig>
</sec>
<sec id="S3.SS6">
<title>Promoter Region Analysis</title>
<p>Promoter elements are necessary for the regulation of gene expression under different conditions. Therefore, we performed the <italic>cis</italic>-regulatory analyses of <italic>TLPs</italic> to foresee their regulatory mechanisms. Based on their putative functions, the identified <italic>cis</italic>-regulatory elements were segregated into four groups; growth and development, light, hormone, and stress-responsive elements (<xref ref-type="supplementary-material" rid="FS1">Supplementary Table 1</xref>). The promoter regions of <italic>TLP</italic> genes comprised of several growth-related elements including TE2F2NTPCNA, EBOX, RYREPEAT4, RAV1AAT, POLLEN1LEAAT52, and so on. In the case of light-responsive elements, GT1CONSENSUS, GATA box, GBOXLERBCS, BOXII, and IBOXCORE were some common <italic>cis</italic>-regulatory elements. However, under the hormonal responsive category, DPBFCOREDCD3, ARFAT, ARR1, ERELEE4, and GARE10OSREP1 were abscisic acid, auxin, cytokinin, ethylene, and gibberellic acid-responsive elements, respectively.</p>
</sec>
<sec id="S3.SS7">
<title>Expression Profiling of the Thaumatin-Like Protein Genes Under Different Tissues and Developmental Stages</title>
<p>Expression analysis of genes is a significant way to understand their involvement in various developmental and physiological processes. Previously, <italic>TLPs</italic> are reported to be involved in plant growth and developmental processes (<xref ref-type="bibr" rid="B47">Munis et al., 2010</xref>; <xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>). Therefore, we performed the expression analysis of <italic>TLPs</italic> under various tissues and their developmental stages using the high-throughput RNA-seq data retrieved from the URGI database and Expression ATLAS (<xref ref-type="bibr" rid="B6">Choulet et al., 2014</xref>; <xref ref-type="bibr" rid="B57">Pingault et al., 2015</xref>; <xref ref-type="bibr" rid="B52">Papatheodorou et al., 2018</xref>). A total of 23, 27, 37, 84, and 29 <italic>TLP</italic> genes showed expression in one or more tissue developmental stages in <italic>B. distachyon, O. sativa, S. bicolor, T. aestivum</italic>, and <italic>Z. mays</italic>, respectively (<xref ref-type="fig" rid="F5">Figures 5A&#x2013;E</xref>). Based on expression profile, these genes were clustered into 3&#x2013;5 groups in various crop species. <italic>BdTLPs</italic> of group 1 were highly expressed in early and emerging inflorescence stages, while <italic>BdTLP9</italic> and <italic>BdTLP12</italic>, and <italic>BdTLP20</italic> and <italic>BdTLP23</italic> were upregulated in endosperm and embryo, respectively. Group 2 genes were highly expressed in the leaf, pistil, embryo, and endosperm tissues. However, group 3 genes were highly expressed at 10 days after pollination (DAP) of seeds; moreover, <italic>BdTLP8</italic> and <italic>BdTLP18</italic> were upregulated in the pistil, as well (<xref ref-type="fig" rid="F5">Figure 5A</xref>). In <italic>O. sativa</italic>, the majority of group 1 genes were highly expressed in seed, group 2 in callus, group 3 genes in the shoot, group 4 in inflorescence, and group 5 genes in emerging inflorescence and anther (<xref ref-type="fig" rid="F5">Figure 5B</xref>). In <italic>S. bicolor</italic>, group 1 and group 4 genes showed higher expression in root and leaf tissues, respectively. However, groups 2 and 3 <italic>TLP</italic> genes were highly expressed in various reproductive tissues like anther, pistil, endosperm, embryo, and flower (<xref ref-type="fig" rid="F5">Figure 5C</xref>).</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption><p>Expression analysis of <italic>TLP</italic> genes of <italic>B. distachyon</italic> (<italic>BdTLP</italic>), <italic>O. sativa</italic> (<italic>OsTLP</italic>). <italic>S. bicolor</italic> (<italic>SbTLP</italic>), <italic>T. aestivum</italic> (<italic>TaTLP</italic>), and <italic>Z. mays</italic> (<italic>ZmTLP</italic>) under various tissue and developmental stages. Heat maps <bold>(A&#x2013;E)</bold> show the clustering and expression profiling of <italic>TLP</italic> genes in <bold>(A)</bold> <italic>B. distachyon</italic>, <bold>(B)</bold> <italic>O. sativa</italic>, <bold>(C)</bold> <italic>S. bicolor</italic>, <bold>(D)</bold> <italic>T. aestivum</italic>, and <bold>(E)</bold> <italic>Z. mays</italic>. The different clusters are formed based on expression values of <italic>TLP</italic> genes in the respective crop, which are represented with different colors. The color bar depicts the upregulated and downregulated expression with red and green colors, respectively.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-12-807448-g005.tif"/>
</fig>
<p>In <italic>T. aestivum</italic>, the majority of group 1 genes exhibited higher expression in root tissue followed by the shoot. However, most of the groups 2, 3, and 4 <italic>TLP</italic> genes were highly expressed in various developmental stages of spike and grain tissues (<xref ref-type="fig" rid="F5">Figure 5D</xref>).</p>
<p>In the case of <italic>Z. mays</italic>, group 1 genes showed significant expression in unpollinated silk, pericarp, and aleurone layer. While the majority of group 2 genes were specifically upregulated in the root tissues, and group 4 genes in the leaf and internode tissues. Group 3 genes were specifically upregulated in the embryo (<xref ref-type="fig" rid="F5">Figure 5E</xref>). These results suggested the role of <italic>TLP</italic> genes in both vegetative and reproductive tissues development in all the studied cereal crops. However, the higher expression of a few genes in a specific tissue or developmental stages suggested their precise role in particular tissue development.</p>
</sec>
<sec id="S3.SS8">
<title>Expression Profiling of the <italic>TaTLP</italic> Genes Under Biotic and Abiotic Stress Conditions</title>
<p>Since TLPs belong to the defense-related protein family and are well known for their stress-responsive behavior. Therefore, the expression analysis of <italic>TaTLP</italic> genes was also performed under various biotic and abiotic stress conditions to reveal their roles in stress resistance (<xref ref-type="bibr" rid="B81">Zhang et al., 2014</xref>, <xref ref-type="bibr" rid="B84">2016</xref>; <xref ref-type="bibr" rid="B42">Liu et al., 2015</xref>). For biotic stress, the available RNA-seq data generated at 24, 48, and 72 h of infestation of two important fungal pathogens, namely, Bgt and Pst were used for expression analysis (<xref ref-type="bibr" rid="B81">Zhang et al., 2014</xref>). In <italic>T. aestivum</italic>, a total of 50 <italic>TaTLP</italic> genes exhibited differential expression (&#x2265; 2 fold) in these stress conditions, which could be clustered into four groups (<xref ref-type="fig" rid="F6">Figure 6A</xref>). The majority of group 1 <italic>TaTLP</italic> genes were upregulated at 24 and 48 h of Bgt infestation. However, all the group 3 and 4 <italic>TaTLP</italic> genes were significantly upregulated at the late (72 h) and early (24 h) periods of Pst infestations, respectively. <italic>TaTLP3-A2</italic>, <italic>TaTLP12-A</italic>, and <italic>TaTLP32-A</italic> were the most upregulated genes after Bgt infection with 37, 36, and 35 folds, respectively. However, in the case of Pst infestation, <italic>TaTLP10-A</italic> (51 fold up) and <italic>TaTLP27-D</italic> (17 fold up) were highly upregulated.</p>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption><p>Expression profiling of <italic>TLP</italic> genes of <italic>T. aestivum</italic> under biotic and abiotic stress conditions. Heat maps <bold>(A&#x2013;C</bold>) show the clustering and expression profiling of <italic>TaTLP</italic> genes under <bold>(A)</bold> <italic>Blumeria graminis</italic> (Bgt) and <italic>Puccinia striiformis</italic> (Pst), <bold>(B)</bold> heat (HS), osmotic (OS), and combined heat and osmotic (HO), and <bold>(C)</bold> salt stress conditions. The clustering of <italic>TaTLP</italic> genes in each heat map is based on their expression pattern in respective stress conditions. The color bar shows high and low expressions with red and green colors, respectively.</p></caption>
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<p>Abiotic stresses are another major threat to plants, which affect various physiological and biological processes. To understand the putative role of <italic>TaTLPs</italic> under abiotic stress conditions, expression analysis was carried out under osmotic (OS), heat (HS), and combined heat and osmotic (HO) stresses using online available RNA-seq data (<xref ref-type="bibr" rid="B42">Liu et al., 2015</xref>). A total of 52 <italic>TaTLPs</italic> exhibited significant differential expression in these stresses, which formed four clusters in the heat map (<xref ref-type="fig" rid="F6">Figure 6B</xref>). Almost all the genes of group 1 were downregulated in the OS, HS, and HO stresses, except <italic>TaTLP12-A</italic> that was slightly upregulated in OS treatment. In the case of group 2, the majority of genes were upregulated at 6 h of OS, HS, and HO treatments, while either unaffected or downregulated at 1 h of treatment. These might be the late responsive <italic>TaTLP</italic> genes. Most of the group 3 and group 4 <italic>TaTLP</italic> genes were found to be OS and HS responsive, respectively.</p>
<p>Expression analysis of the <italic>TaTLP</italic> genes was also performed at 6, 12, 24, and 48 h of salt stress using available RNA-seq data (<xref ref-type="bibr" rid="B84">Zhang et al., 2016</xref>). Out of 93 genes, 63 <italic>TaTLP</italic> genes were found to be differentially expressed under salt stress, which were clustered into 4 groups, based on their expression patterns (<xref ref-type="fig" rid="F6">Figure 6C</xref>). All the group 1 genes were downregulated at all the stages of salt stress treatment. In contrast, all the group 3 genes were found significantly upregulated at 48 h of treatment. However, group 2 genes were upregulated at the early stage (6 h) of treatment, while they get normalized at later stages. The results suggested that the group 2 and group 3 genes are early and late responsive <italic>TaTLP</italic> genes, respectively.</p>
<p>In addition to <italic>in silico</italic> analysis, qRT-PCR analyses of eight <italic>TaTLP</italic> genes were performed using the gene-specific primers at similar heat, osmotic, and salt stress treatments for the validation of expression profile (<xref ref-type="fig" rid="F7">Figures 7A&#x2013;P</xref> and <xref ref-type="supplementary-material" rid="FS1">Supplementary File 5</xref>). Overall, the result was in agreement with the expression observed using RNA-seq data, with a few exceptions. In the case of heat stress, <italic>TaTLP2-B</italic>, <italic>TaTLP7-D</italic>, <italic>TaTLP14-B1</italic>, and <italic>TaTLP25-B</italic> were more upregulated at 1 h, while other genes were highly upregulated at 6 h of treatment. In the case of osmotic stress, <italic>TaTLP-7D</italic> was exclusively more upregulated at 1 h, whereas other genes were upregulated at 6 h. However, <italic>TaTLP2-B</italic> and <italic>TaTLP10-D</italic> were downregulated at OS 1 h. The majority of genes were highly upregulated at 1 h HO treatment. In the case of salt stress, seven genes were highly upregulated at 12 h of salt stress, except <italic>TaTLP14-B1</italic> that showed maximum expression at 48 h. The results further confirmed that a few <italic>TaTLP</italic> genes are early while others are late responsive.</p>
<fig id="F7" position="float">
<label>FIGURE 7</label>
<caption><p>qRT-PCR analysis of eight <italic>TaTLP</italic> genes. Expression patterns in the form of fold changes have been shown in the bar graphs. <bold>(A,C,E,G,I,K,M,O)</bold> Show expression of <italic>TaTLP2-B</italic>, <italic>TaTLP5-D, TaTLP7-D, TaTLP9-D, TaTLP10-D, TaTLP14-B1, TaTLP25-B, and TaTLP29-A</italic> genes, under HS, OS, and HO stress conditions, while <bold>(B,D,F,H,J,L,N,P)</bold> shows the expression pattern of these genes under salt stress, respectively. Significance between the control and treated conditions is carried using a two-tailed student&#x2019;s <italic>t</italic>-test. The ns, &#x002A;, &#x002A;&#x002A;, and &#x002A;&#x002A;&#x002A; markings represent the significance at <italic>p</italic>-value &#x003E; 0.05, &#x2264;0.05, &#x2264;0.01, &#x2264;0.001, respectively.</p></caption>
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<sec id="S3.SS9">
<title>Comparative Expression Profiling of the <italic>TaTLP</italic> Paralogous Genes</title>
<p>To understand the function of duplicated genes, a comparative expression profiling of each paralogous pair was performed. Generally, based on expression pattern, duplicated genes could categorize into the retention of function, pseudo-functionalization, and neo-functionalization. Out of the six paralogous gene pairs, three pairs (<italic>TaTLP1-A-TaTLP24-D, TaTLP1-B-TaTLP24-B</italic>, and <italic>TaTLP15-A-TaTLP18-B</italic>) showed a similar trend of expression, which suggested retention of function in these duplicated genes (<xref ref-type="fig" rid="F8">Figures 8A&#x2013;C</xref>). Two duplicated pairs (<italic>TaTLP12-D-TaTLP13-D</italic> and <italic>TaTLP16-A-TaTLP17-A</italic>) showed insignificant expression of one of the gene suggested pseudo-functionalization (<xref ref-type="fig" rid="F8">Figures 8D,E</xref>). Retention of function in the majority of duplicated genes and the absence of neo-functionalization suggested functional conservation in <italic>TLP</italic> genes during evolution.</p>
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<label>FIGURE 8</label>
<caption><p>Comparative expression analysis of duplicated gene pairs in <italic>T. aestivum</italic>. <bold>(A&#x2013;E)</bold> Represent the comparative expression pattern of paralogous <italic>TaTLPs</italic> under various tissue and developmental stages. Based on their expression trend, <italic>TaTLPs</italic> are categorized into the retention of function <bold>(A&#x2013;C)</bold> and pseudo functionalization types <bold>(D,E)</bold>.</p></caption>
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<sec id="S3.SS10">
<title>Cloning and Functional Characterization of the <italic>TaTLP2-B</italic> in <italic>Saccharomyces cerevisiae</italic></title>
<p>In our study, since the <italic>TaTLP2-B</italic> exhibited significant differential expression under abiotic stress conditions, it was selected for functional characterization. <italic>TaTLP2-B</italic> ORF was amplified using end primers and cloned into the pYES2.1 yeast expression vector. The <italic>LacZ</italic> gene-containing vector was used as a control (<xref ref-type="fig" rid="F9">Figures 9A&#x2013;F</xref>). In the spot assay, we observed similar growth of both control (LacZ) and TaTLP2-B expressing yeast cells in the controlled conditions (<xref ref-type="fig" rid="F9">Figure 9A</xref>). Since the yeast optimum growth temperature is 30&#x00B0;C, we used 37 and 40&#x00B0;C for heat stress treatment. However, we observed higher growth inhibition at 40&#x00B0;C treatment, therefore, 37&#x00B0;C treatment was used for further analysis. In the case of 20% PEG, we could not see significant difference at the lower dilutions, therefore 30% PEG was used for further analysis. Similarly, less than 1 M NaCl could not cause significant inhibition at lower dilutions. The results revealed that in the case of cold (4&#x00B0;C), osmotic (30% PEG), heat, combined heat and osmotic (37&#x00B0;C and 30% PEG), and salt (1M NaCl) stress conditions, TaTLP2-B recombinant cells exhibited higher growth than the control cells (<xref ref-type="fig" rid="F9">Figures 9B&#x2013;F</xref>). The results suggested that the overexpression of the TaTLP2-B provided abiotic stress tolerance to the recombinant yeast cells. This gene can be used for the development of abiotic stress-resistant transgenic crops in future studies.</p>
<fig id="F9" position="float">
<label>FIGURE 9</label>
<caption><p>Spot assay of recombinant <italic>Saccharomyces cerevisiae</italic> (yeast) cells under various stress conditions. <bold>(A)</bold> Shows similar growth of both TaTLP2-B (pYES2.1-TaTLP2-B) and control vector (pYES2.1/V5-His/lacZ) containing yeast cells under control conditions. <bold>(B&#x2013;F)</bold> Shows the spot assay analysis of <italic>TaTLP2-B</italic> and control vector containing yeast cells in <bold>(B)</bold> cold (4&#x00B0;C), <bold>(C)</bold> osmotic (30% PEG), <bold>(D)</bold> heat (37&#x00B0;C), <bold>(E)</bold> combined heat and osmotic (37&#x00B0;C and 30% PEG), and <bold>(F)</bold> salt (1M NaCl) stress conditions, respectively.</p></caption>
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<sec id="S4" sec-type="discussion">
<title>Discussion</title>
<p>Thaumatin-like proteins are important proteins involved in the tissue development and stress resistance pathways of plants (<xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>). Therefore, we have studied the TLPs in five major cereals including <italic>B</italic>. <italic>distachyon</italic>, <italic>O</italic>. <italic>sativa</italic>, <italic>S</italic>. <italic>bicolor</italic>, <italic>T</italic>. <italic>aestivum</italic>, and <italic>Z</italic>. <italic>mays</italic>. In the present study, we have identified a total of 26, 27, 39, 93, and 37 <italic>TLPs</italic> in the genome of <italic>B</italic>. <italic>distachyon</italic>, <italic>O</italic>. <italic>sativa</italic>, <italic>S</italic>. <italic>bicolor</italic>, <italic>T</italic>. <italic>aestivum</italic> and <italic>Z</italic>. <italic>mays</italic>, respectively. Variable numbers of the <italic>TLP</italic> genes in different plants have been reported in earlier studies. For instance, 24, 33, and 49 <italic>TLP</italic> genes have been reported in diploid <italic>A</italic>. <italic>thaliana</italic>, <italic>Vitis vinifera</italic>, and <italic>Populus trichocarpa</italic>, respectively (<xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>; <xref ref-type="bibr" rid="B78">Yan et al., 2017</xref>). In the case of <italic>O</italic>. <italic>sativa</italic> and <italic>Z</italic>. <italic>mays</italic>, 49 <italic>TLP</italic> genes in each are reported in the earlier study (<xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>), because probably they had not removed the genes with incomplete thaumatin signature motifs, as done in the present study. The occurrence of the highest number of <italic>TLP</italic> genes in <italic>T</italic>. <italic>aestivum</italic> could be attributed to their complex allohexaploid genome configuration (AABBDD) (<xref ref-type="bibr" rid="B64">Sharma A. et al., 2020</xref>). Further, differential expansion of the <italic>TLP</italic> genes in various plant species might be attributed to the number of DEs.</p>
<p>The duplication events are responsible for the expansion of gene families and these are the major forces to attain neo-functionality by causing genetic variability (<xref ref-type="bibr" rid="B3">Appels et al., 2018</xref>). In DEs analysis, our results suggested that tandem DEs are a major factor in <italic>B</italic>. <italic>distachyon</italic>, <italic>O</italic>. <italic>sativa</italic>, and <italic>S</italic>. <italic>bicolor</italic> and segmental DEs in <italic>T</italic>. <italic>aestivum</italic> and <italic>Z</italic>. <italic>mays</italic> behind the gene expansion of TLP family. The role of tandem and segmental duplications in the evolution of TLP gene family has been earlier reported in various plant species including <italic>A</italic>. <italic>thaliana</italic>, <italic>O</italic>. <italic>sativa</italic>, and <italic>Z</italic>. <italic>mays</italic> (<xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>). The higher number of paralogous genes in <italic>T</italic>. <italic>aestivum</italic> and <italic>Z</italic>. <italic>mays</italic> might be attributed to their larger genome size and the presence of more transposable elements (<xref ref-type="bibr" rid="B18">Gaut, 2002</xref>; <xref ref-type="bibr" rid="B13">Ellegren, 2008</xref>).</p>
<p>Furthermore, the divergence time of monocots from eudicots was estimated as &#x223C;170&#x2013;235 Mya, which were further diverged into grasses around &#x223C;77 Mya (<xref ref-type="bibr" rid="B79">Yang et al., 1999</xref>; <xref ref-type="bibr" rid="B18">Gaut, 2002</xref>). Therefore, the paralogous <italic>TLP</italic> genes in <italic>B</italic>. <italic>distachyon</italic> might have evolved before the divergence of grasses. The main duplication incidence in <italic>S</italic>. <italic>bicolor</italic> and <italic>O</italic>. <italic>sativa</italic> genome was estimated at around &#x223C;70 Mya (<xref ref-type="bibr" rid="B54">Paterson et al., 2004</xref>). However, our results indicated that the majority of paralogous <italic>TLP</italic> genes of <italic>O</italic>. <italic>sativa</italic> and <italic>S</italic>. <italic>bicolor</italic> are evolved after the main DE occurrence. In <italic>Z</italic>. <italic>mays</italic>, paralogous <italic>TLP</italic> genes were probably formed close to the divergence time of maize and sorghum, i.e., &#x223C;11&#x2013;28 Mya (<xref ref-type="bibr" rid="B54">Paterson et al., 2004</xref>). However, in the case of <italic>T</italic>. <italic>aestivum</italic>, paralogous <italic>TLP</italic> genes were probably evolved earlier than the hybridization event of A, B, and D subgenomes (<xref ref-type="bibr" rid="B45">Marcussen et al., 2014</xref>). However, two duplicated pairs, having NUP 96 domain, showed their recent incidence of DEs, which showed that TLPs might be acquiring the new functions over the course of evolution. Duplicated genes face various environmental forces and natural pressures during the process of evolution (<xref ref-type="bibr" rid="B13">Ellegren, 2008</xref>). Our results suggested the purifying selection of <italic>TLP</italic> genes as a major force of selection, as reported in the various other plant species (<xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>; <xref ref-type="bibr" rid="B41">Liu et al., 2020</xref>). Moreover, positive selection has also been reported for <italic>TLP</italic> genes in poplar, which suggested the role of varied natural selection procedures during TLPs&#x2019; evolution (<xref ref-type="bibr" rid="B40">Liu et al., 2010b</xref>). Since the TLPs are paraphyletic in origin, they are supposed to be derived from multiple ancestral genes (<xref ref-type="bibr" rid="B67">Shatters et al., 2006</xref>). Clustering of identified TLPs in multiple clades is in agreement with the paraphyletic nature of origin. Further, a variable number of TLPs in each clade is due to the differential duplication of <italic>TLP</italic> genes. Similarly, the uneven distribution and paraphyletic nature of TLPs have also been reported by previous studies (<xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>; <xref ref-type="bibr" rid="B41">Liu et al., 2020</xref>). The tight clustering of homeologous and paralogous genes could be due to the high sequence homology among the respective sequences.</p>
<p>The organization of introns and exons of <italic>TLPs</italic> have been reported to be in the range of one to ten exons (<xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>; <xref ref-type="bibr" rid="B56">Petre et al., 2011</xref>; <xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>). On similar patterns, our results suggest comparable findings with one to four exons in most of the TLPs. However, most of the monocots&#x2019; TLPs have intron-less nature, which was also found in our analysis (<xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>). Additionally, our results with respect to the protein lengths, MWs, and isoelectric points of long and small TLP proteins were found in accordance with previously studied TLPs (<xref ref-type="bibr" rid="B39">Liu et al., 2010a</xref>; <xref ref-type="bibr" rid="B56">Petre et al., 2011</xref>; <xref ref-type="bibr" rid="B5">Cao et al., 2016</xref>). In our analysis, the TaTLP2-B was found to be localized in the extracellular region. Similarly, the extracellular localization of a wheat TLP (TaLr19TLP1) is also reported in an earlier study (<xref ref-type="bibr" rid="B82">Zhang et al., 2018</xref>).</p>
<p>In addition, the presence of thaumatin-like domain in all the TLP proteins, make our studies similar to previously reported findings. However, four ZmTLPs (ZmTLP16, ZmTLP20, ZmTLP25, and ZmTLP33) have an additional NUP 96 domain. The NUP 96 domain is reported to be involved in plant development and stress resistance against pathogens (<xref ref-type="bibr" rid="B83">Zhang and Li, 2005</xref>). Various abiotic and biotic stress-responsive elements were also found in most of the studied <italic>TLPs</italic>, for instance, DRE2COREZMRAB17, ASF1, BIHD1, CBFHV, CGG-box, GCCCORE, LTRECOREATCOR15, MYB, MYC, WRKY1, W-box, T/G-box, and so on. Various plant hormone-related and stress-related <italic>cis</italic>-regulatory elements have also been reported in four cotton species (<xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>). Moreover, in previous studies, the elements like ERE, W-box, and WRKY were found to be involved in plant growth and stress resistance (<xref ref-type="bibr" rid="B20">Gou et al., 2007</xref>; <xref ref-type="bibr" rid="B26">Hiroyuki and Terauchi, 2008</xref>; <xref ref-type="bibr" rid="B59">Rushton et al., 2010</xref>). The occurrence of numerous <italic>cis</italic>-regulatory elements suggested diverse functions of <italic>TLP</italic> genes in plants. Further, the expression profiling of <italic>TLPs</italic> under various tissues and developmental stages also advocated the putative involvement of these genes in the development of vegetative and reproductive tissues. Similar expression trend in various plant tissues and their role in reproductive tissues like flowers and seeds has also been reported in earlier studies; for instance, <italic>TLP</italic> genes in <italic>Gossypium hirsutum</italic> also showed their varied expression pattern in vegetative as well as in reproductive organs (<xref ref-type="bibr" rid="B16">Fils-Lycaon et al., 1996</xref>; <xref ref-type="bibr" rid="B63">Seo et al., 2008</xref>; <xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>).</p>
<p>The role of <italic>TLP</italic> genes in fungal resistance has been reported in earlier studies against numerous pathogens including <italic>Bipolaris sorokiniana</italic> (<xref ref-type="bibr" rid="B10">Cui et al., 2021</xref>), <italic>Fusarium</italic> sp. (<xref ref-type="bibr" rid="B44">Mackintosh et al., 2007</xref>), <italic>Microdochium nivale</italic> (<xref ref-type="bibr" rid="B34">Kuwabara et al., 2002</xref>), <italic>Puccinia. Triticina</italic> (<xref ref-type="bibr" rid="B10">Cui et al., 2021</xref>), <italic>Rhizoctonia solani</italic> (<xref ref-type="bibr" rid="B49">Naseri et al., 2012</xref>), and <italic>Verticillium dahlia</italic> (<xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>) in wheat and other plant species. Bioassay of <italic>Plasmopara viticola</italic> in transgenic <italic>V. vinifera</italic> showed that the overexpression of <italic>VaTLP</italic> gene helped in the reduction of hyphe growth (<xref ref-type="bibr" rid="B24">He et al., 2017</xref>). The exact mechanism of TLPs is ambiguous; however, in the oomycetes fungus, PR5 are reported to degrade the &#x03B2;-1,3-glucans (<xref ref-type="bibr" rid="B1">Abad et al., 1996</xref>; <xref ref-type="bibr" rid="B21">Grenier et al., 1999</xref>). Moreover, a recent study also showed the interaction of <italic>TaTLP1</italic> with <italic>PR1</italic> genes of <italic>T. aestivum</italic> in two-hybrid experiments (Y2H) (<xref ref-type="bibr" rid="B76">Wang et al., 2020</xref>). The differential expression of <italic>TaTLP</italic> genes in response to Pst and Bgt infestation further established their roles in fungal stress responses.</p>
<p>The qRT-PCR of a few selected genes was carried out to validate the expression data obtained from the RNA-seq analyses. The <italic>TaARF</italic> gene was used as an internal control as reported in earlier studies (<xref ref-type="bibr" rid="B68">Shumayla et al., 2019</xref>; <xref ref-type="bibr" rid="B72">Tyagi et al., 2021</xref>). Further, the RNA-seq data analysis revealed invariable expression of <italic>TaARF</italic> gene in all the tissue developmental stages and stress conditions, therefore it was used as a reference gene in our qRT-PCR analyses. The qRT-PCR results showed the variable expression of <italic>TaTLPs</italic> at early and late stages of heat, osmotic, and combined heat and osmotic and salt stress treatments. The expression trends were similar as observed in RNA-seq data. For instance, <italic>TaTLP5-D</italic> exhibited the maximum expression at 6 h of osmotic and combined heat and osmotic stresses, and 12 h of salt stress in both qRT-PCR and <italic>in silico</italic> expression analyses. Similarly, in the case of <italic>TaTLP14-B1</italic> and <italic>TaTLP29-A</italic>, the maximum upregulation was seen at the later stages of osmotic and salt stresses in both the RNA-seq data and qRT-PCR results. These results supported the consistency in the expression data of RNA-seq and qRT-PCR, and suggested the stress-responsive nature of <italic>TaTLP</italic> genes. Further, the <italic>TaTLP2-B</italic> exhibited significant differential expression in various stress conditions, therefore it was used for cloning and functional characterization in yeast. Moreover, similar to our <italic>in silico</italic> and qRT-PCR finding&#x2019;s differential expression, upregulation of <italic>TLP</italic> genes at various hours of osmotic, salt, and cold stress treatment has also been reported in other plants like <italic>Brassica rapa</italic> and <italic>Gossypium</italic> sp. (<xref ref-type="bibr" rid="B2">Ahmed et al., 2013</xref>; <xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>). Seven genes of <italic>B. rapa</italic> (<italic>BrTLP1, 2, 3, 8, 12, 13, and 20</italic>) exhibited differential expression at the different time intervals of cold, drought, and salt stresses (<xref ref-type="bibr" rid="B2">Ahmed et al., 2013</xref>). Moreover, the qRT-PCR experiment showed the upregulation of <italic>BoTLP1</italic> of <italic>Brassica oleracea</italic> L. var. <italic>Italica</italic> after 4, 8, and 24 h of salt (200 mM Nacl) and drought stresses (300 mM mannitol) (<xref ref-type="bibr" rid="B23">He et al., 2021</xref>).</p>
<p>The overexpression of <italic>TaTLP2-B</italic> provided significant tolerance against various abiotic stress conditions in yeast cells. Similarly, the overexpression of <italic>TLP</italic> genes provided increased tolerance against various abiotic stresses in tobacco, cotton, Arabidopsis, broccoli, and so on (<xref ref-type="bibr" rid="B58">Rajam et al., 2007</xref>; <xref ref-type="bibr" rid="B46">Misra et al., 2016</xref>; <xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>; <xref ref-type="bibr" rid="B23">He et al., 2021</xref>). In a recently conducted study, the important role of a cotton <italic>TLP</italic> (<italic>GhTLP19</italic>) gene was studied in combating drought stress (<xref ref-type="bibr" rid="B38">Li Z. et al., 2020</xref>). Moreover, the <italic>GbTLP1</italic> of <italic>G</italic>. <italic>barbadense</italic> and <italic>ObTLP1</italic> of <italic>Ocimum basilicum</italic> were found effective against drought and salt stresses in two separate studies (<xref ref-type="bibr" rid="B47">Munis et al., 2010</xref>; <xref ref-type="bibr" rid="B46">Misra et al., 2016</xref>). The transgenic line of <italic>Brassica oleracea L. var. Italica</italic> with overexpressed <italic>BolTLP1</italic> showed remarkable resistance against drought and salt stresses (<xref ref-type="bibr" rid="B23">He et al., 2021</xref>). The abscisic acid (ABA) signaling cascade is a central pathway in the regulation of salt, drought, and other abiotic stresses. In a recent study, thaumatin mutant plants showed alteration in the ABA signaling pathway, which ultimately leads to increased susceptibility of plants to abiotic stresses (<xref ref-type="bibr" rid="B53">Park and Kim, 2021</xref>). Collectively, these findings depict that the TLP proteins could be utilized to develop stress resistant transgenic cereal crops, which will be a boost for future agriculture.</p>
</sec>
<sec sec-type="conclusion" id="S5">
<title>Conclusions</title>
<p>Thaumatin-like proteins, a part of the PR5 protein family, are known to be involved in various biotic and abiotic stresses. The curiosity to unravel the various possibilities led us to a detailed characterization of a total of 222 <italic>TLP</italic> genes in five cereal crops. Phylogenetic analysis revealed the paraphyletic origin of TLPs in cereals, while the occurrence of DEs suggested the role of paralogous genes in the expansion of the TLP gene family. Gene expression analysis using RNA-seq data and qRT-PCR suggested the important roles of <italic>TLP</italic> genes in plant growth and development and abiotic and biotic stress responses. Significant tolerance in the <italic>TaTLP2-B</italic> expressing yeast cells further established their role in stress response. Overall, the study revealed that the <italic>TLP</italic> genes can be used for stress-resistant transgenic crop development. Since the identified genes are directly derived from the food crops, they would be easily deregulated from the regulatory authority of the transgenic crops. Further, the current study will facilitate the detailed functional characterization of <italic>TLP</italic> genes of cereal crops in future studies.</p>
</sec>
<sec id="S6" sec-type="data-availability">
<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: URGI, <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="PRJNA243835">PRJNA243835</ext-link>; NCBI BioProject, <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="PRJNA243835">PRJNA243835</ext-link>, <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="SRP045409">SRP045409</ext-link>, and <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="SRP062745">SRP062745</ext-link>.</p>
</sec>
<sec id="S7">
<title>Author Contributions</title>
<p>SU conceived the idea. AS and SU designed the experiments. AS, HS, and RR performed the experiments. AS, HS, and AP analyzed the data. AS, HS, and SU wrote the manuscript. All authors have read and finalized the manuscript.</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>
<ack>
<p>We are grateful to the Panjab University, Chandigarh, and National Institute of Plant Genome Research, New Delhi, India, for research facilities, Ensembl Plants, URGI, and NCBI for data availability. AS and HS is grateful to CSIR for the senior research fellowship.</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.2021.807448/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fpls.2021.807448/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Data_Sheet_1.ZIP" id="FS1" mimetype="application/zip" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Figure 1</label>
<caption><p>Multiple sequence alignment of 222 Thaumatin-like proteins (TLPs) of <italic>B. distachyon, O. sativa, S. bicolor</italic>, <italic>T. aestivum</italic>, and <italic>Z. mays</italic>. Conserved cysteine residues are marked with an asterisk. The red dot denotes the REDDD motif. The FF hydrophobic motif is highlighted with a green triangle. The thaumatin signature motif, conserved domain, and amino acids forming the bottom of the acidic cleft are marked with sky blue, red, and brown lines, respectively.</p></caption>
</supplementary-material>
<supplementary-material xlink:href="Data_Sheet_1.ZIP" id="FS2" mimetype="application/zip" xmlns:xlink="http://www.w3.org/1999/xlink">
<label>Supplementary Figure 2</label>
<caption><p>Intron/exon organization and conserved motifs of TLPs of <italic>B. distachyon</italic>, <italic>O. sativa</italic>, <italic>S. bicolor, T. aestivum</italic>, and <italic>Z. mays</italic>.</p></caption>
</supplementary-material>
</sec>
<ref-list>
<title>References</title>
<ref id="B1"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Abad</surname> <given-names>L. R.</given-names></name> <name><surname>D&#x2019;Urzo</surname> <given-names>M. P.</given-names></name> <name><surname>Liu</surname> <given-names>D.</given-names></name> <name><surname>Narasimhan</surname> <given-names>M. L.</given-names></name> <name><surname>Reuveni</surname> <given-names>M.</given-names></name> <name><surname>Zhu</surname> <given-names>J. K.</given-names></name><etal/></person-group> (<year>1996</year>). <article-title>Antifungal activity of tobacco osmotin has specificity and involves plasma membrane permeabilization.</article-title> <source><italic>Plant Sci.</italic></source> <volume>118</volume> <fpage>11</fpage>&#x2013;<lpage>23</lpage>. <pub-id pub-id-type="doi">10.1016/0168-9452(96)04420-2</pub-id></citation></ref>
<ref id="B2"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ahmed</surname> <given-names>N. U.</given-names></name> <name><surname>Park</surname> <given-names>J.-I.</given-names></name> <name><surname>Jung</surname> <given-names>H.-J.</given-names></name> <name><surname>Kang</surname> <given-names>K.-K.</given-names></name> <name><surname>Lim</surname> <given-names>Y.-P.</given-names></name> <name><surname>Hur</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>Molecular characterization of thaumatin family genes related to stresses in <italic>Brassica rapa</italic>.</article-title> <source><italic>Sci. Hortic.</italic></source> <volume>152</volume> <fpage>26</fpage>&#x2013;<lpage>34</lpage>. <pub-id pub-id-type="doi">10.1016/j.scienta.2013.01.007</pub-id></citation></ref>
<ref id="B3"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Appels</surname> <given-names>R.</given-names></name> <name><surname>Eversole</surname> <given-names>K.</given-names></name> <name><surname>Stein</surname> <given-names>N.</given-names></name> <name><surname>Feuillet</surname> <given-names>C.</given-names></name> <name><surname>Keller</surname> <given-names>B.</given-names></name> <name><surname>Rogers</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Shifting the limits in wheat research and breeding using a fully annotated reference genome.</article-title> <source><italic>Science</italic></source> <volume>361</volume>:<issue>eaar7191</issue>. <pub-id pub-id-type="doi">10.1126/science.aar7191</pub-id> <pub-id pub-id-type="pmid">30115783</pub-id></citation></ref>
<ref id="B4"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bailey</surname> <given-names>T. L.</given-names></name> <name><surname>Boden</surname> <given-names>M.</given-names></name> <name><surname>Buske</surname> <given-names>F. A.</given-names></name> <name><surname>Frith</surname> <given-names>M.</given-names></name> <name><surname>Grant</surname> <given-names>C. E.</given-names></name> <name><surname>Clementi</surname> <given-names>L.</given-names></name><etal/></person-group> (<year>2009</year>). <article-title>MEME SUITE: tools for motif discovery and searching.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>37</volume> <fpage>W202</fpage>&#x2013;<lpage>W208</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkp335</pub-id> <pub-id pub-id-type="pmid">19458158</pub-id></citation></ref>
<ref id="B5"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cao</surname> <given-names>J.</given-names></name> <name><surname>Lv</surname> <given-names>Y.</given-names></name> <name><surname>Hou</surname> <given-names>Z.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Ding</surname> <given-names>L.</given-names></name></person-group> (<year>2016</year>). <article-title>Expansion and evolution of thaumatin-like protein (TLP) gene family in six plants.</article-title> <source><italic>Plant Growth Regul.</italic></source> <volume>79</volume> <fpage>299</fpage>&#x2013;<lpage>307</lpage>. <pub-id pub-id-type="doi">10.1007/s10725-015-0134-y</pub-id></citation></ref>
<ref id="B6"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Choulet</surname> <given-names>F.</given-names></name> <name><surname>Alberti</surname> <given-names>A.</given-names></name> <name><surname>Theil</surname> <given-names>S.</given-names></name> <name><surname>Glover</surname> <given-names>N. M.</given-names></name> <name><surname>Barbe</surname> <given-names>V.</given-names></name> <name><surname>Daron</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>Structural and functional partitioning of bread wheat chromosome 3B.</article-title> <source><italic>Science</italic></source> <volume>345</volume>:<issue>1250092</issue>.</citation></ref>
<ref id="B7"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Christensen</surname> <given-names>A. B.</given-names></name> <name><surname>Cho</surname> <given-names>B. H.</given-names></name> <name><surname>Naesby</surname> <given-names>M.</given-names></name> <name><surname>Gregersen</surname> <given-names>P. L.</given-names></name> <name><surname>Brandt</surname> <given-names>J.</given-names></name> <name><surname>Madriz-Ordenana</surname> <given-names>K.</given-names></name><etal/></person-group> (<year>2002</year>). <article-title>The molecular characterization of two barley proteins establishes the novel PR-17 family of pathogenesis-related proteins.</article-title> <source><italic>Mol. Plant Pathol.</italic></source> <volume>3</volume> <fpage>135</fpage>&#x2013;<lpage>144</lpage>. <pub-id pub-id-type="doi">10.1046/j.1364-3703.2002.00105.x</pub-id> <pub-id pub-id-type="pmid">20569319</pub-id></citation></ref>
<ref id="B8"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Corpet</surname> <given-names>F.</given-names></name></person-group> (<year>1988</year>). <article-title>Multiple sequence alignment with hierarchical clustering.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>16</volume> <fpage>10881</fpage>&#x2013;<lpage>10890</lpage>.</citation></ref>
<ref id="B9"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cserzo</surname> <given-names>M.</given-names></name> <name><surname>Eisenhaber</surname> <given-names>F.</given-names></name> <name><surname>Eisenhaber</surname> <given-names>B.</given-names></name> <name><surname>Simon</surname> <given-names>I.</given-names></name></person-group> (<year>2004</year>). <article-title>TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.</article-title> <source><italic>Bioinformatics</italic></source> <volume>20</volume> <fpage>136</fpage>&#x2013;<lpage>137</lpage>. <pub-id pub-id-type="doi">10.1093/bioinformatics/btg394</pub-id> <pub-id pub-id-type="pmid">14693825</pub-id></citation></ref>
<ref id="B10"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cui</surname> <given-names>Z.</given-names></name> <name><surname>Liang</surname> <given-names>F.</given-names></name> <name><surname>Zhang</surname> <given-names>J.</given-names></name> <name><surname>Wang</surname> <given-names>F.</given-names></name> <name><surname>Liu</surname> <given-names>D.</given-names></name> <name><surname>Wang</surname> <given-names>H.</given-names></name></person-group> (<year>2021</year>). <article-title>Transgenic expression of TaTLP1, a thaumatin-like protein gene, reduces susceptibility to common root rot and leaf rust in wheat.</article-title> <source><italic>Crop J.</italic></source> <volume>9</volume> <fpage>1214</fpage>&#x2013;<lpage>1218</lpage>. <pub-id pub-id-type="doi">10.1016/J.CJ.2021.03.021</pub-id></citation></ref>
<ref id="B11"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Datta</surname> <given-names>K.</given-names></name> <name><surname>Velazhahan</surname> <given-names>R.</given-names></name> <name><surname>Oliva</surname> <given-names>N.</given-names></name> <name><surname>Ona</surname> <given-names>I.</given-names></name> <name><surname>Mew</surname> <given-names>T.</given-names></name> <name><surname>Khush</surname> <given-names>G. S.</given-names></name><etal/></person-group> (<year>1999</year>). <article-title>Over-expression of the cloned rice thaumatin-like protein (PR-5) gene in transgenic rice plants enhances environmental friendly resistance to <italic>Rhizoctonia solani</italic> causing sheath blight disease.</article-title> <source><italic>Theor. Appl. Genet.</italic></source> <volume>98</volume> <fpage>1138</fpage>&#x2013;<lpage>1145</lpage>. <pub-id pub-id-type="doi">10.1007/s001220051178</pub-id></citation></ref>
<ref id="B12"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Edgar</surname> <given-names>R. C.</given-names></name></person-group> (<year>2004</year>). <article-title>MUSCLE: multiple sequence alignment with high accuracy and high throughput.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>32</volume> <fpage>1792</fpage>&#x2013;<lpage>1797</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkh340</pub-id> <pub-id pub-id-type="pmid">15034147</pub-id></citation></ref>
<ref id="B13"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ellegren</surname> <given-names>H.</given-names></name></person-group> (<year>2008</year>). <article-title>Comparative genomics and the study of evolution by natural selection.</article-title> <source><italic>Mol. Ecol.</italic></source> <volume>17</volume> <fpage>4586</fpage>&#x2013;<lpage>4596</lpage>. <pub-id pub-id-type="doi">10.1111/j.1365-294X.2008.03954.x</pub-id> <pub-id pub-id-type="pmid">19140982</pub-id></citation></ref>
<ref id="B14"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Emanuelsson</surname> <given-names>O.</given-names></name> <name><surname>Nielsen</surname> <given-names>H.</given-names></name> <name><surname>Brunak</surname> <given-names>S.</given-names></name> <name><surname>Von Heijne</surname> <given-names>G.</given-names></name></person-group> (<year>2000</year>). <article-title>Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.</article-title> <source><italic>J. Mol. Biol.</italic></source> <volume>300</volume> <fpage>1005</fpage>&#x2013;<lpage>1016</lpage>. <pub-id pub-id-type="doi">10.1006/jmbi.2000.3903</pub-id> <pub-id pub-id-type="pmid">10891285</pub-id></citation></ref>
<ref id="B15"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fierens</surname> <given-names>E.</given-names></name> <name><surname>Gebruers</surname> <given-names>K.</given-names></name> <name><surname>Voet</surname> <given-names>A. R. D.</given-names></name> <name><surname>De Maeyer</surname> <given-names>M.</given-names></name> <name><surname>Courtin</surname> <given-names>C. M.</given-names></name> <name><surname>Delcour</surname> <given-names>J. A.</given-names></name></person-group> (<year>2009</year>). <article-title>Biochemical and structural characterization of TLXI, the <italic>Triticum aestivum</italic> L. thaumatin-like xylanase inhibitor.</article-title> <source><italic>J. Enzyme Inhib. Med. Chem.</italic></source> <volume>24</volume> <fpage>646</fpage>&#x2013;<lpage>654</lpage>. <pub-id pub-id-type="doi">10.1080/14756360802321831</pub-id> <pub-id pub-id-type="pmid">18951281</pub-id></citation></ref>
<ref id="B16"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fils-Lycaon</surname> <given-names>B. R.</given-names></name> <name><surname>Wiersma</surname> <given-names>P. A.</given-names></name> <name><surname>Eastwell</surname> <given-names>K. C.</given-names></name> <name><surname>Sautiere</surname> <given-names>P.</given-names></name></person-group> (<year>1996</year>). <article-title>A cherry protein and its gene, abundantly expressed in ripening fruit, have been identified as thaumatin-like.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>111</volume> <fpage>269</fpage>&#x2013;<lpage>273</lpage>.</citation></ref>
<ref id="B17"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gasteiger</surname> <given-names>E.</given-names></name> <name><surname>Hoogland</surname> <given-names>C.</given-names></name> <name><surname>Gattiker</surname> <given-names>A.</given-names></name> <name><surname>Duvaud</surname> <given-names>S.</given-names></name> <name><surname>Wilkins</surname> <given-names>M. R.</given-names></name> <name><surname>Appel</surname> <given-names>R. D.</given-names></name><etal/></person-group> (<year>2005</year>). &#x201C;<article-title>Protein identification and analysis tools on the ExPASy Server</article-title>,&#x201D; in <source><italic>The Proteomics Protocols Handbook</italic></source>, <role>ed.</role> <person-group person-group-type="editor"><name><surname>Walker</surname> <given-names>J. M.</given-names></name></person-group> (<publisher-loc>Totowa, NJ</publisher-loc>: <publisher-name>Humana Press</publisher-name>).</citation></ref>
<ref id="B18"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gaut</surname> <given-names>B. S.</given-names></name></person-group> (<year>2002</year>). <article-title>Evolutionary dynamics of grass genomes.</article-title> <source><italic>New Phytol.</italic></source> <volume>154</volume> <fpage>15</fpage>&#x2013;<lpage>28</lpage>. <pub-id pub-id-type="doi">10.1046/j.1469-8137.2002.00352.x</pub-id></citation></ref>
<ref id="B19"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gaut</surname> <given-names>B. S.</given-names></name> <name><surname>Morton</surname> <given-names>B. R.</given-names></name> <name><surname>McCaig</surname> <given-names>B. C.</given-names></name> <name><surname>Clegg</surname> <given-names>M. T.</given-names></name></person-group> (<year>1996</year>). <article-title>Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.</article-title> <source><italic>Proc. Natl. Acad. Sci. U.S.A.</italic></source> <volume>93</volume>:<issue>10274</issue>. <pub-id pub-id-type="doi">10.1073/PNAS.93.19.10274</pub-id> <pub-id pub-id-type="pmid">8816790</pub-id></citation></ref>
<ref id="B20"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gou</surname> <given-names>J. Y.</given-names></name> <name><surname>Wang</surname> <given-names>L. J.</given-names></name> <name><surname>Chen</surname> <given-names>S. P.</given-names></name> <name><surname>Hu</surname> <given-names>W. L.</given-names></name> <name><surname>Chen</surname> <given-names>X. Y.</given-names></name></person-group> (<year>2007</year>). <article-title>Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis.</article-title> <source><italic>Cell Res.</italic></source> <volume>17</volume> <fpage>422</fpage>&#x2013;<lpage>434</lpage>. <pub-id pub-id-type="doi">10.1038/sj.cr.7310150</pub-id> <pub-id pub-id-type="pmid">17387330</pub-id></citation></ref>
<ref id="B21"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Grenier</surname> <given-names>J.</given-names></name> <name><surname>Potvin</surname> <given-names>C.</given-names></name> <name><surname>Trudel</surname> <given-names>J.</given-names></name> <name><surname>Asselin</surname> <given-names>A.</given-names></name></person-group> (<year>1999</year>). <article-title>Some thaumatin-like proteins hydrolyse polymeric &#x03B2;-1,3-glucans.</article-title> <source><italic>Plant J.</italic></source> <volume>19</volume> <fpage>473</fpage>&#x2013;<lpage>480</lpage>. <pub-id pub-id-type="doi">10.1046/J.1365-313X.1999.00551.X</pub-id> <pub-id pub-id-type="pmid">10504569</pub-id></citation></ref>
<ref id="B22"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Haas</surname> <given-names>B. J.</given-names></name> <name><surname>Papanicolaou</surname> <given-names>A.</given-names></name> <name><surname>Yassour</surname> <given-names>M.</given-names></name> <name><surname>Grabherr</surname> <given-names>M.</given-names></name> <name><surname>Blood</surname> <given-names>P. D.</given-names></name> <name><surname>Bowden</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.</article-title> <source><italic>Nat. Protoc.</italic></source> <volume>8</volume> <fpage>1494</fpage>&#x2013;<lpage>1512</lpage>. <pub-id pub-id-type="doi">10.1038/nprot.2013.084</pub-id> <pub-id pub-id-type="pmid">23845962</pub-id></citation></ref>
<ref id="B23"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>He</surname> <given-names>L.</given-names></name> <name><surname>Li</surname> <given-names>L.</given-names></name> <name><surname>Zhu</surname> <given-names>Y.</given-names></name> <name><surname>Pan</surname> <given-names>Y.</given-names></name> <name><surname>Zhang</surname> <given-names>X.</given-names></name> <name><surname>Han</surname> <given-names>X.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Boltlp1, a thaumatin-like protein gene, confers tolerance to salt and drought stresses in broccoli (<italic>Brassica oleracea</italic> l. var. italica).</article-title> <source><italic>Int. J. Mol. Sci.</italic></source> <volume>22</volume>:<issue>11132</issue>. <pub-id pub-id-type="doi">10.3390/IJMS222011132/S1</pub-id></citation></ref>
<ref id="B24"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>He</surname> <given-names>R.</given-names></name> <name><surname>Wu</surname> <given-names>J.</given-names></name> <name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Ag&#x00FC;ero</surname> <given-names>C. B.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Liu</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Overexpression of a thaumatin-like protein gene from <italic>Vitis amurensis</italic> improves downy mildew resistance in <italic>Vitis vinifera</italic> grapevine.</article-title> <source><italic>Protoplasma</italic></source> <volume>254</volume>, <fpage>1579</fpage>&#x2013;<lpage>1589</lpage>. <pub-id pub-id-type="doi">10.1007/s00709-016-1047-y</pub-id> <pub-id pub-id-type="pmid">27900595</pub-id></citation></ref>
<ref id="B25"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Higo</surname> <given-names>K.</given-names></name> <name><surname>Ugawa</surname> <given-names>Y.</given-names></name> <name><surname>Iwamoto</surname> <given-names>M.</given-names></name> <name><surname>Higo</surname> <given-names>H.</given-names></name></person-group> (<year>1998</year>). <article-title>PLACE: a database of plant cis -acting regulatory DNA elements.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>26</volume> <fpage>358</fpage>&#x2013;<lpage>359</lpage>.</citation></ref>
<ref id="B26"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hiroyuki</surname> <given-names>K.</given-names></name> <name><surname>Terauchi</surname> <given-names>R.</given-names></name></person-group> (<year>2008</year>). <article-title>Regulation of expression of rice thaumatin-like protein: inducibility by elicitor requires promoter W-box elements.</article-title> <source><italic>Plant Cell Rep.</italic></source> <volume>27</volume> <fpage>1521</fpage>&#x2013;<lpage>1528</lpage>. <pub-id pub-id-type="doi">10.1007/s00299-008-0536-7</pub-id> <pub-id pub-id-type="pmid">18425517</pub-id></citation></ref>
<ref id="B27"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Horton</surname> <given-names>P.</given-names></name> <name><surname>Park</surname> <given-names>K.-J.</given-names></name> <name><surname>Obayashi</surname> <given-names>T.</given-names></name> <name><surname>Fujita</surname> <given-names>N.</given-names></name> <name><surname>Harada</surname> <given-names>H.</given-names></name> <name><surname>Adams-Collier</surname> <given-names>C. J.</given-names></name><etal/></person-group> (<year>2007</year>). <article-title>WoLF PSORT: protein localization predictor.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>35</volume> <fpage>W585</fpage>&#x2013;<lpage>W587</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkm259</pub-id> <pub-id pub-id-type="pmid">17517783</pub-id></citation></ref>
<ref id="B28"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hu</surname> <given-names>B.</given-names></name> <name><surname>Jin</surname> <given-names>J.</given-names></name> <name><surname>Guo</surname> <given-names>A.-Y.</given-names></name> <name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Luo</surname> <given-names>J.</given-names></name> <name><surname>Gao</surname> <given-names>G.</given-names></name></person-group> (<year>2015</year>). <article-title>GSDS 2.0: an upgraded gene feature visualization server.</article-title> <source><italic>Bioinformatics</italic></source> <volume>31</volume> <fpage>1296</fpage>&#x2013;<lpage>1297</lpage>. <pub-id pub-id-type="doi">10.1093/bioinformatics/btu817</pub-id> <pub-id pub-id-type="pmid">25504850</pub-id></citation></ref>
<ref id="B29"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname> <given-names>S.</given-names></name> <name><surname>Sirikhachornkit</surname> <given-names>A.</given-names></name> <name><surname>Su</surname> <given-names>X.</given-names></name> <name><surname>Faris</surname> <given-names>J.</given-names></name> <name><surname>Gill</surname> <given-names>B.</given-names></name> <name><surname>Haselkorn</surname> <given-names>R.</given-names></name><etal/></person-group> (<year>2002</year>). <article-title>Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat.</article-title> <source><italic>Proc. Natl. Acad. Sci. U.S.A.</italic></source> <volume>99</volume> <fpage>8133</fpage>&#x2013;<lpage>8138</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.072223799</pub-id> <pub-id pub-id-type="pmid">12060759</pub-id></citation></ref>
<ref id="B30"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>K&#x00E4;ll</surname> <given-names>L.</given-names></name> <name><surname>Krogh</surname> <given-names>A.</given-names></name> <name><surname>Sonnhammer</surname> <given-names>E. L.</given-names></name></person-group> (<year>2004</year>). <article-title>A combined transmembrane topology and signal peptide prediction method.</article-title> <source><italic>J. Mol. Biol.</italic></source> <volume>338</volume> <fpage>1027</fpage>&#x2013;<lpage>1036</lpage>. <pub-id pub-id-type="doi">10.1016/j.jmb.2004.03.016</pub-id> <pub-id pub-id-type="pmid">15111065</pub-id></citation></ref>
<ref id="B31"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>King</surname> <given-names>B. R.</given-names></name> <name><surname>Guda</surname> <given-names>C.</given-names></name></person-group> (<year>2007</year>). <article-title>ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes.</article-title> <source><italic>Genome Biol.</italic></source> <volume>8</volume>:<issue>R68</issue>. <pub-id pub-id-type="doi">10.1186/gb-2007-8-5-r68</pub-id> <pub-id pub-id-type="pmid">17472741</pub-id></citation></ref>
<ref id="B32"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kombrink</surname> <given-names>E.</given-names></name> <name><surname>Somssich</surname> <given-names>I. E.</given-names></name></person-group> (<year>1997</year>). &#x201C;<article-title>Pathogenesis-related proteins and plant defense</article-title>,&#x201D; in <source><italic>Plant Relationships</italic></source>, <role>ed.</role> <person-group person-group-type="editor"><name><surname>Deising</surname> <given-names>H. B.</given-names></name></person-group> (<publisher-loc>Berlin</publisher-loc>: <publisher-name>Springer</publisher-name>), <fpage>107</fpage>&#x2013;<lpage>128</lpage>.</citation></ref>
<ref id="B33"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kumar</surname> <given-names>S.</given-names></name> <name><surname>Stecher</surname> <given-names>G.</given-names></name> <name><surname>Li</surname> <given-names>M.</given-names></name> <name><surname>Knyaz</surname> <given-names>C.</given-names></name> <name><surname>Tamura</surname> <given-names>K.</given-names></name></person-group> (<year>2018</year>). <article-title>MEGA X: molecular evolutionary genetics analysis across computing platforms.</article-title> <source><italic>Mol. Biol. Evol.</italic></source> <volume>35</volume> <fpage>1547</fpage>&#x2013;<lpage>1549</lpage>.</citation></ref>
<ref id="B34"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kuwabara</surname> <given-names>C.</given-names></name> <name><surname>Takezawa</surname> <given-names>D.</given-names></name> <name><surname>Shimada</surname> <given-names>T.</given-names></name> <name><surname>Hamada</surname> <given-names>T.</given-names></name> <name><surname>Fujikawa</surname> <given-names>S.</given-names></name> <name><surname>Arakawa</surname> <given-names>K.</given-names></name></person-group> (<year>2002</year>). <article-title>Abscisic acid- and cold-induced thaumatin-like protein in winter wheat has an antifungal activity against snow mould, <italic>Microdochium nivale</italic>.</article-title> <source><italic>Physiol. Plant.</italic></source> <volume>115</volume> <fpage>101</fpage>&#x2013;<lpage>110</lpage>. <pub-id pub-id-type="doi">10.1034/j.1399-3054.2002.1150112.x</pub-id> <pub-id pub-id-type="pmid">12010473</pub-id></citation></ref>
<ref id="B35"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lei</surname> <given-names>P.</given-names></name> <name><surname>Wei</surname> <given-names>X.</given-names></name> <name><surname>Gao</surname> <given-names>R.</given-names></name> <name><surname>Huo</surname> <given-names>F.</given-names></name> <name><surname>Nie</surname> <given-names>X.</given-names></name> <name><surname>Tong</surname> <given-names>W.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>Genome-wide identification of PYL gene family in wheat: evolution, expression and 3D structure analysis.</article-title> <source><italic>Genomics</italic></source> <volume>113</volume> <fpage>854</fpage>&#x2013;<lpage>866</lpage>. <pub-id pub-id-type="doi">10.1016/j.ygeno.2020.12.017</pub-id> <pub-id pub-id-type="pmid">33321205</pub-id></citation></ref>
<ref id="B36"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Letunic</surname> <given-names>I.</given-names></name> <name><surname>Doerks</surname> <given-names>T.</given-names></name> <name><surname>Bork</surname> <given-names>P.</given-names></name></person-group> (<year>2015</year>). <article-title>SMART: recent updates, new developments and status in 2015.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>43</volume> <fpage>D257</fpage>&#x2013;<lpage>D260</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gku949</pub-id> <pub-id pub-id-type="pmid">25300481</pub-id></citation></ref>
<ref id="B37"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Li</surname> <given-names>S.</given-names></name> <name><surname>Qiu</surname> <given-names>B.</given-names></name> <name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Cui</surname> <given-names>X.</given-names></name> <name><surname>Ge</surname> <given-names>F.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Thaumatin-like protein genes of Panax notoginseng confers resistance to <italic>Alternaria panax</italic>.</article-title> <source><italic>Physiol. Mol. Plant Pathol.</italic></source> <volume>112</volume>:<issue>101537</issue>. <pub-id pub-id-type="doi">10.1016/J.PMPP.2020.101537</pub-id></citation></ref>
<ref id="B38"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>Z.</given-names></name> <name><surname>Wang</surname> <given-names>X.</given-names></name> <name><surname>Cui</surname> <given-names>Y.</given-names></name> <name><surname>Qiao</surname> <given-names>K.</given-names></name> <name><surname>Zhu</surname> <given-names>L.</given-names></name> <name><surname>Fan</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Comprehensive genome-wide analysis of thaumatin-like gene family in four cotton species and functional identification of GhTLP19 involved in regulating tolerance to <italic>Verticillium dahlia</italic> and drought.</article-title> <source><italic>Front. Plant Sci.</italic></source> <volume>11</volume>:<issue>575015</issue>. <pub-id pub-id-type="doi">10.3389/fpls.2020.575015</pub-id> <pub-id pub-id-type="pmid">33193513</pub-id></citation></ref>
<ref id="B39"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>J.-J.</given-names></name> <name><surname>Sturrock</surname> <given-names>R.</given-names></name> <name><surname>Ekramoddoullah</surname> <given-names>A. K. M.</given-names></name></person-group> (<year>2010a</year>). <article-title>The superfamily of thaumatin-like proteins: its origin, evolution, and expression towards biological function.</article-title> <source><italic>Plant Cell Rep.</italic></source> <volume>29</volume> <fpage>419</fpage>&#x2013;<lpage>436</lpage>. <pub-id pub-id-type="doi">10.1007/s00299-010-0826-8</pub-id> <pub-id pub-id-type="pmid">20204373</pub-id></citation></ref>
<ref id="B40"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>J.-J.</given-names></name> <name><surname>Zamani</surname> <given-names>A.</given-names></name> <name><surname>Ekramoddoullah</surname> <given-names>A. K. M.</given-names></name></person-group> (<year>2010b</year>). <article-title>Expression profiling of a complex thaumatin-like protein family in western white pine.</article-title> <source><italic>Planta</italic></source> <volume>231</volume> <fpage>637</fpage>&#x2013;<lpage>651</lpage>. <pub-id pub-id-type="doi">10.1007/s00425-009-1068-2</pub-id> <pub-id pub-id-type="pmid">19997927</pub-id></citation></ref>
<ref id="B41"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>Y.</given-names></name> <name><surname>Cui</surname> <given-names>J.</given-names></name> <name><surname>Zhou</surname> <given-names>X.</given-names></name> <name><surname>Luan</surname> <given-names>Y.</given-names></name> <name><surname>Luan</surname> <given-names>F.</given-names></name></person-group> (<year>2020</year>). <article-title>Genome-wide identification, characterization and expression analysis of the TLP gene family in melon (<italic>Cucumis melo</italic> L.).</article-title> <source><italic>Genomics</italic></source> <volume>112</volume> <fpage>2499</fpage>&#x2013;<lpage>2509</lpage>. <pub-id pub-id-type="doi">10.1016/j.ygeno.2020.02.001</pub-id> <pub-id pub-id-type="pmid">32044327</pub-id></citation></ref>
<ref id="B42"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>Z.</given-names></name> <name><surname>Xin</surname> <given-names>M.</given-names></name> <name><surname>Qin</surname> <given-names>J.</given-names></name> <name><surname>Peng</surname> <given-names>H.</given-names></name> <name><surname>Ni</surname> <given-names>Z.</given-names></name> <name><surname>Yao</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (<italic>Triticum aestivum</italic> L.).</article-title> <source><italic>BMC Plant Biol.</italic></source> <volume>15</volume>:<issue>152</issue>. <pub-id pub-id-type="doi">10.1186/s12870-015-0511-8</pub-id> <pub-id pub-id-type="pmid">26092253</pub-id></citation></ref>
<ref id="B43"><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="B44"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mackintosh</surname> <given-names>C. A.</given-names></name> <name><surname>Lewis</surname> <given-names>J.</given-names></name> <name><surname>Radmer</surname> <given-names>L. E.</given-names></name> <name><surname>Shin</surname> <given-names>S.</given-names></name> <name><surname>Heinen</surname> <given-names>S. J.</given-names></name> <name><surname>Smith</surname> <given-names>L. A.</given-names></name><etal/></person-group> (<year>2007</year>). <article-title>Overexpression of defense response genes in transgenic wheat enhances resistance to Fusarium head blight.</article-title> <source><italic>Plant Cell Rep.</italic></source> <volume>26</volume> <fpage>479</fpage>&#x2013;<lpage>488</lpage>. <pub-id pub-id-type="doi">10.1007/s00299-006-0265-8</pub-id> <pub-id pub-id-type="pmid">17103001</pub-id></citation></ref>
<ref id="B45"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Marcussen</surname> <given-names>T.</given-names></name> <name><surname>Sandve</surname> <given-names>S. R.</given-names></name> <name><surname>Heier</surname> <given-names>L.</given-names></name> <name><surname>Spannagl</surname> <given-names>M.</given-names></name> <name><surname>Pfeifer</surname> <given-names>M.</given-names></name> <name><surname>Jakobsen</surname> <given-names>K. S.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>Ancient hybridizations among the ancestral genomes of bread wheat.</article-title> <source><italic>Science</italic></source> <volume>345</volume>:<issue>1250092</issue>. <pub-id pub-id-type="doi">10.1126/science.1250092</pub-id> <pub-id pub-id-type="pmid">25035499</pub-id></citation></ref>
<ref id="B46"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Misra</surname> <given-names>R. C.</given-names></name> <name><surname>Sandeep</surname></name> <name><surname>Kamthan</surname> <given-names>M.</given-names></name> <name><surname>Kumar</surname> <given-names>S.</given-names></name> <name><surname>Ghosh</surname> <given-names>S.</given-names></name></person-group> (<year>2016</year>). <article-title>A thaumatin-like protein of <italic>Ocimum basilicum</italic> confers tolerance to fungal pathogen and abiotic stress in transgenic <italic>Arabidopsis</italic>.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>6</volume>:<issue>25340</issue>. <pub-id pub-id-type="doi">10.1038/srep25340</pub-id> <pub-id pub-id-type="pmid">27150014</pub-id></citation></ref>
<ref id="B47"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Munis</surname> <given-names>M. F. H.</given-names></name> <name><surname>Tu</surname> <given-names>L.</given-names></name> <name><surname>Deng</surname> <given-names>F.</given-names></name> <name><surname>Tan</surname> <given-names>J.</given-names></name> <name><surname>Xu</surname> <given-names>L.</given-names></name> <name><surname>Xu</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2010</year>). <article-title>A thaumatin-like protein gene involved in cotton fiber secondary cell wall development enhances resistance against Verticillium dahliae and other stresses in transgenic tobacco.</article-title> <source><italic>Biochem. Biophys. Res. Commun.</italic></source> <volume>393</volume> <fpage>38</fpage>&#x2013;<lpage>44</lpage>. <pub-id pub-id-type="doi">10.1016/j.bbrc.2010.01.069</pub-id> <pub-id pub-id-type="pmid">20097164</pub-id></citation></ref>
<ref id="B48"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Nagaraju</surname> <given-names>M.</given-names></name> <name><surname>Reddy</surname> <given-names>P. S.</given-names></name> <name><surname>Kumar</surname> <given-names>S. A.</given-names></name> <name><surname>Kumar</surname> <given-names>A.</given-names></name> <name><surname>Rajasheker</surname> <given-names>G.</given-names></name> <name><surname>Rao</surname> <given-names>D. M.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Genome-wide identification and transcriptional profiling of small heat shock protein gene family under diverse abiotic stress conditions in <italic>Sorghum bicolor</italic> (L.).</article-title> <source><italic>Int. J. Biol. Macromol.</italic></source> <volume>142</volume> <fpage>822</fpage>&#x2013;<lpage>834</lpage>. <pub-id pub-id-type="doi">10.1016/j.ijbiomac.2019.10.023</pub-id> <pub-id pub-id-type="pmid">31622710</pub-id></citation></ref>
<ref id="B49"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Naseri</surname> <given-names>G.</given-names></name> <name><surname>Sohani</surname> <given-names>M. M.</given-names></name> <name><surname>Pourmassalehgou</surname> <given-names>A.</given-names></name> <name><surname>Allahi</surname> <given-names>S.</given-names></name></person-group> (<year>2012</year>). <article-title>In planta transformation of rice (Oryza sativa) using thaumatin-like protein gene for enhancing resistance to sheath blight.</article-title> <source><italic>Afr. J. Biotechnol.</italic></source> <volume>11</volume> <fpage>7885</fpage>&#x2013;<lpage>7893</lpage>. <pub-id pub-id-type="doi">10.5897/AJB11.3331</pub-id></citation></ref>
<ref id="B50"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Neale</surname> <given-names>A. D.</given-names></name> <name><surname>Wahleithner</surname> <given-names>J. A.</given-names></name> <name><surname>Lund</surname> <given-names>M.</given-names></name> <name><surname>Bonnett</surname> <given-names>H. T.</given-names></name> <name><surname>Kelly</surname> <given-names>A.</given-names></name> <name><surname>Meeks-Wagner</surname> <given-names>D. R.</given-names></name><etal/></person-group> (<year>1990</year>). <article-title>Chitinase, [beta]-1,3-glucanase, osmotin, and extensin Are expressed in tobacco explants during flower formation.</article-title> <source><italic>Plant cell online</italic></source> <volume>2</volume> <fpage>673</fpage>&#x2013;<lpage>684</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.2.7.673</pub-id> <pub-id pub-id-type="pmid">2152343</pub-id></citation></ref>
<ref id="B51"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Nussbaumer</surname> <given-names>T.</given-names></name> <name><surname>Martis</surname> <given-names>M. M.</given-names></name> <name><surname>Roessner</surname> <given-names>S. K.</given-names></name> <name><surname>Pfeifer</surname> <given-names>M.</given-names></name> <name><surname>Bader</surname> <given-names>K. C.</given-names></name> <name><surname>Sharma</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>MIPS PlantsDB: a database framework for comparative plant genome research.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>41</volume> <fpage>D1144</fpage>&#x2013;<lpage>D1151</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gks1153</pub-id> <pub-id pub-id-type="pmid">23203886</pub-id></citation></ref>
<ref id="B52"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Papatheodorou</surname> <given-names>I.</given-names></name> <name><surname>Fonseca</surname> <given-names>N. A.</given-names></name> <name><surname>Keays</surname> <given-names>M.</given-names></name> <name><surname>Tang</surname> <given-names>Y. A.</given-names></name> <name><surname>Barrera</surname> <given-names>E.</given-names></name> <name><surname>Bazant</surname> <given-names>W.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Expression Atlas: gene and protein expression across multiple studies and organisms.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>46</volume> <fpage>D246</fpage>&#x2013;<lpage>D251</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkx1158</pub-id> <pub-id pub-id-type="pmid">29165655</pub-id></citation></ref>
<ref id="B53"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Park</surname> <given-names>E. J.</given-names></name> <name><surname>Kim</surname> <given-names>T. H.</given-names></name></person-group> (<year>2021</year>). <article-title>Thaumatin-like genes function in the control of both biotic stress signaling and ABA signaling pathways.</article-title> <source><italic>Biochem. Biophys. Res. Commun.</italic></source> <volume>567</volume> <fpage>17</fpage>&#x2013;<lpage>21</lpage>. <pub-id pub-id-type="doi">10.1016/J.BBRC.2021.06.012</pub-id> <pub-id pub-id-type="pmid">34130180</pub-id></citation></ref>
<ref id="B54"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Paterson</surname> <given-names>A. H.</given-names></name> <name><surname>Bowers</surname> <given-names>J. E.</given-names></name> <name><surname>Chapman</surname> <given-names>B. A.</given-names></name></person-group> (<year>2004</year>). <article-title>Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics.</article-title> <source><italic>Proc. Natl. Acad. Sci. U.S.A.</italic></source> <volume>101</volume> <fpage>9903</fpage>&#x2013;<lpage>9908</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.0307901101</pub-id> <pub-id pub-id-type="pmid">15161969</pub-id></citation></ref>
<ref id="B55"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Petersen</surname> <given-names>T. N.</given-names></name> <name><surname>Brunak</surname> <given-names>S.</given-names></name> <name><surname>von Heijne</surname> <given-names>G.</given-names></name> <name><surname>Nielsen</surname> <given-names>H.</given-names></name></person-group> (<year>2011</year>). <article-title>SignalP 4.0: discriminating signal peptides from transmembrane regions.</article-title> <source><italic>Nat. Methods</italic></source> <volume>8</volume> <fpage>785</fpage>&#x2013;<lpage>786</lpage>. <pub-id pub-id-type="doi">10.1038/nmeth.1701</pub-id> <pub-id pub-id-type="pmid">21959131</pub-id></citation></ref>
<ref id="B56"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Petre</surname> <given-names>B.</given-names></name> <name><surname>Major</surname> <given-names>I.</given-names></name> <name><surname>Rouhier</surname> <given-names>N.</given-names></name> <name><surname>Duplessis</surname> <given-names>S.</given-names></name></person-group> (<year>2011</year>). <article-title>Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar.</article-title> <source><italic>BMC Plant Biol.</italic></source> <volume>11</volume>:<issue>33</issue>. <pub-id pub-id-type="doi">10.1186/1471-2229-11-33</pub-id> <pub-id pub-id-type="pmid">21324123</pub-id></citation></ref>
<ref id="B57"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pingault</surname> <given-names>L.</given-names></name> <name><surname>Choulet</surname> <given-names>F.</given-names></name> <name><surname>Alberti</surname> <given-names>A.</given-names></name> <name><surname>Glover</surname> <given-names>N.</given-names></name> <name><surname>Wincker</surname> <given-names>P.</given-names></name> <name><surname>Feuillet</surname> <given-names>C.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.</article-title> <source><italic>Genome Biol.</italic></source> <volume>16</volume>:<issue>29</issue>. <pub-id pub-id-type="doi">10.1186/s13059-015-0601-9</pub-id> <pub-id pub-id-type="pmid">25853487</pub-id></citation></ref>
<ref id="B58"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Rajam</surname> <given-names>M. V.</given-names></name> <name><surname>Chandola</surname> <given-names>N.</given-names></name> <name><surname>Saiprasad Goud</surname> <given-names>P.</given-names></name> <name><surname>Singh</surname> <given-names>D.</given-names></name> <name><surname>Kashyap</surname> <given-names>V.</given-names></name> <name><surname>Choudhary</surname> <given-names>M. L.</given-names></name><etal/></person-group> (<year>2007</year>). <article-title>Thaumatin gene confers resistance to fungal pathogens as well as tolerance to abiotic stresses in transgenic tobacco plants.</article-title> <source><italic>Biol. Plant.</italic></source> <volume>51</volume> <fpage>135</fpage>&#x2013;<lpage>141</lpage>. <pub-id pub-id-type="doi">10.1007/s10535-007-0026-8</pub-id></citation></ref>
<ref id="B59"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Rushton</surname> <given-names>P. J.</given-names></name> <name><surname>Somssich</surname> <given-names>I. E.</given-names></name> <name><surname>Ringler</surname> <given-names>P.</given-names></name> <name><surname>Shen</surname> <given-names>Q. J.</given-names></name></person-group> (<year>2010</year>). <article-title>WRKY transcription factors.</article-title> <source><italic>Trends Plant Sci.</italic></source> <volume>15</volume> <fpage>247</fpage>&#x2013;<lpage>258</lpage>. <pub-id pub-id-type="doi">10.1016/j.tplants.2010.02.006</pub-id> <pub-id pub-id-type="pmid">20304701</pub-id></citation></ref>
<ref id="B60"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sakamoto</surname> <given-names>Y.</given-names></name> <name><surname>Watanabe</surname> <given-names>H.</given-names></name> <name><surname>Nagai</surname> <given-names>M.</given-names></name> <name><surname>Nakade</surname> <given-names>K.</given-names></name> <name><surname>Takahashi</surname> <given-names>M.</given-names></name> <name><surname>Sato</surname> <given-names>T.</given-names></name></person-group> (<year>2006</year>). <article-title>Lentinula edodes tlg1 encodes a thaumatin-like protein that is involved in lentinan degradation and fruiting body senescence.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>141</volume> <fpage>793</fpage>&#x2013;<lpage>801</lpage>. <pub-id pub-id-type="doi">10.1104/pp.106.076679</pub-id> <pub-id pub-id-type="pmid">16648221</pub-id></citation></ref>
<ref id="B61"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Salzman</surname> <given-names>R. A.</given-names></name> <name><surname>Tikhonova</surname> <given-names>I.</given-names></name> <name><surname>Bordelon</surname> <given-names>B. P.</given-names></name> <name><surname>Hasegawa</surname> <given-names>P. M.</given-names></name> <name><surname>Bressan</surname> <given-names>R. A.</given-names></name></person-group> (<year>1998</year>). <article-title>Coordinate accumulation of antifungal proteins and hexoses constitutes a developmentally controlled defense response during fruit ripening in grape.</article-title> <source><italic>Plant Physiol.</italic></source> <volume>117</volume> <fpage>465</fpage>&#x2013;<lpage>472</lpage>.</citation></ref>
<ref id="B62"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Seo</surname> <given-names>J.</given-names></name> <name><surname>Gordish-Dressman</surname> <given-names>H.</given-names></name> <name><surname>Hoffman</surname> <given-names>E. P.</given-names></name></person-group> (<year>2006</year>). <article-title>An interactive power analysis tool for microarray hypothesis testing and generation.</article-title> <source><italic>Bioinformatics</italic></source> <volume>22</volume> <fpage>808</fpage>&#x2013;<lpage>814</lpage>. <pub-id pub-id-type="doi">10.1093/bioinformatics/btk052</pub-id> <pub-id pub-id-type="pmid">16418236</pub-id></citation></ref>
<ref id="B63"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Seo</surname> <given-names>P. J.</given-names></name> <name><surname>Lee</surname> <given-names>A.-K.</given-names></name> <name><surname>Xiang</surname> <given-names>F.</given-names></name> <name><surname>Park</surname> <given-names>C.-M.</given-names></name></person-group> (<year>2008</year>). <article-title>Molecular and functional profiling of Arabidopsis pathogenesis-related genes: insights into their roles in salt response of seed germination.</article-title> <source><italic>Plant Cell Physiol.</italic></source> <volume>49</volume> <fpage>334</fpage>&#x2013;<lpage>344</lpage>. <pub-id pub-id-type="doi">10.1093/pcp/pcn011</pub-id> <pub-id pub-id-type="pmid">18203731</pub-id></citation></ref>
<ref id="B64"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sharma</surname> <given-names>A.</given-names></name> <name><surname>Shumayla</surname></name> <name><surname>Tyagi</surname> <given-names>S.</given-names></name> <name><surname>Alok</surname> <given-names>A.</given-names></name> <name><surname>Singh</surname> <given-names>K.</given-names></name> <name><surname>Upadhyay</surname> <given-names>S. K.</given-names></name></person-group> (<year>2020</year>). <article-title>Thaumatin-like protein kinases: molecular characterization and transcriptional profiling in five cereal crops.</article-title> <source><italic>Plant Sci.</italic></source> <volume>290</volume>:<issue>110317</issue>. <pub-id pub-id-type="doi">10.1016/j.plantsci.2019.110317</pub-id> <pub-id pub-id-type="pmid">31779910</pub-id></citation></ref>
<ref id="B65"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sharma</surname> <given-names>H.</given-names></name> <name><surname>Taneja</surname> <given-names>M.</given-names></name> <name><surname>Upadhyay</surname> <given-names>S. K.</given-names></name></person-group> (<year>2020</year>). <article-title>Identification, characterization and expression profiling of cation-proton antiporter superfamily in <italic>Triticum aestivum</italic> L. and functional analysis of TaNHX4-B.</article-title> <source><italic>Genomics</italic></source> <volume>112</volume> <fpage>356</fpage>&#x2013;<lpage>370</lpage>. <pub-id pub-id-type="doi">10.1016/j.ygeno.2019.02.015</pub-id> <pub-id pub-id-type="pmid">30818061</pub-id></citation></ref>
<ref id="B66"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sharma</surname> <given-names>M.</given-names></name> <name><surname>Singh</surname> <given-names>A.</given-names></name> <name><surname>Shankar</surname> <given-names>A.</given-names></name> <name><surname>Pandey</surname> <given-names>A.</given-names></name> <name><surname>Baranwal</surname> <given-names>V.</given-names></name> <name><surname>Kapoor</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>Comprehensive expression analysis of rice armadillo gene family during abiotic stress and development.</article-title> <source><italic>DNA Res.</italic></source> <volume>21</volume> <fpage>267</fpage>&#x2013;<lpage>283</lpage>. <pub-id pub-id-type="doi">10.1093/dnares/dst056</pub-id> <pub-id pub-id-type="pmid">24398598</pub-id></citation></ref>
<ref id="B67"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Shatters</surname> <given-names>R. G.</given-names></name> <name><surname>Boykin</surname> <given-names>L. M.</given-names></name> <name><surname>Lapointe</surname> <given-names>S. L.</given-names></name> <name><surname>Hunter</surname> <given-names>W. B.</given-names></name> <name><surname>Weathersbee</surname> <given-names>A. A.</given-names></name></person-group> (<year>2006</year>). <article-title>Phylogenetic and structural relationships of the PR5 gene family reveal an ancient multigene family conserved in plants and select animal taxa.</article-title> <source><italic>J. Mol. Evol.</italic></source> <volume>63</volume> <fpage>12</fpage>&#x2013;<lpage>29</lpage>. <pub-id pub-id-type="doi">10.1007/s00239-005-0053-z</pub-id> <pub-id pub-id-type="pmid">16736102</pub-id></citation></ref>
<ref id="B68"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Shumayla</surname></name> <name><surname>Tyagi</surname> <given-names>S.</given-names></name> <name><surname>Sharma</surname> <given-names>A.</given-names></name> <name><surname>Singh</surname> <given-names>K.</given-names></name> <name><surname>Upadhyay</surname> <given-names>S. K.</given-names></name></person-group> (<year>2019</year>). <article-title>Genomic dissection and transcriptional profiling of cysteine-rich receptor-like kinases in five cereals and functional characterization of TaCRK68-A.</article-title> <source><italic>Int. J. Biol. Macromol.</italic></source> <volume>134</volume> <fpage>316</fpage>&#x2013;<lpage>329</lpage>. <pub-id pub-id-type="doi">10.1016/j.ijbiomac.2019.05.016</pub-id> <pub-id pub-id-type="pmid">31078592</pub-id></citation></ref>
<ref id="B69"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Stothard</surname> <given-names>P.</given-names></name></person-group> (<year>2000</year>). <article-title>The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences.</article-title> <source><italic>Biotechniques</italic></source> <volume>28</volume>:<issue>1104</issue>. <pub-id pub-id-type="doi">10.2144/00286ir01</pub-id> <pub-id pub-id-type="pmid">10868275</pub-id></citation></ref>
<ref id="B70"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Suyama</surname> <given-names>M.</given-names></name> <name><surname>Torrents</surname> <given-names>D.</given-names></name> <name><surname>Bork</surname> <given-names>P.</given-names></name></person-group> (<year>2006</year>). <article-title>PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>34</volume> <fpage>W609</fpage>&#x2013;<lpage>W612</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkl315</pub-id> <pub-id pub-id-type="pmid">16845082</pub-id></citation></ref>
<ref id="B71"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tajima</surname> <given-names>F.</given-names></name></person-group> (<year>1993</year>). <article-title>Simple methods for testing the molecular evolutionary clock hypothesis.</article-title> <source><italic>Genetics</italic></source> <volume>135</volume> <fpage>599</fpage>&#x2013;<lpage>607</lpage>.</citation></ref>
<ref id="B72"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tyagi</surname> <given-names>S.</given-names></name> <name><surname>Shumayla</surname></name> <name><surname>Madhu</surname></name> <name><surname>Singh</surname> <given-names>K.</given-names></name> <name><surname>Upadhyay</surname> <given-names>S. K.</given-names></name></person-group> (<year>2021</year>). <article-title>Molecular characterization revealed the role of catalases under abiotic and arsenic stress in bread wheat (<italic>Triticum aestivum</italic> L.).</article-title> <source><italic>J. Hazardous Mater.</italic></source> <volume>403</volume>:<issue>123585</issue>. <pub-id pub-id-type="doi">10.1016/j.jhazmat.2020.123585</pub-id> <pub-id pub-id-type="pmid">32810714</pub-id></citation></ref>
<ref id="B73"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>van der Wel</surname> <given-names>H.</given-names></name> <name><surname>Loeve</surname> <given-names>K.</given-names></name></person-group> (<year>1972</year>). <article-title>Isolation and characterization of thaumatin I and II, the sweet-tasting proteins from <italic>Thaumatococcus daniellii</italic> Benth.</article-title> <source><italic>Eur. J. Biochem.</italic></source> <volume>31</volume> <fpage>221</fpage>&#x2013;<lpage>225</lpage>. <pub-id pub-id-type="doi">10.1111/j.1432-1033.1972.tb02522.x</pub-id> <pub-id pub-id-type="pmid">4647176</pub-id></citation></ref>
<ref id="B74"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>van Loon</surname> <given-names>L. C.</given-names></name> <name><surname>Rep</surname> <given-names>M.</given-names></name> <name><surname>Pieterse</surname> <given-names>C. M. J.</given-names></name></person-group> (<year>2006</year>). <article-title>Significance of inducible defense-related proteins in infected plants.</article-title> <source><italic>Annu. Rev. Phytopathol.</italic></source> <volume>44</volume> <fpage>135</fpage>&#x2013;<lpage>162</lpage>. <pub-id pub-id-type="doi">10.1146/annurev.phyto.44.070505.143425</pub-id> <pub-id pub-id-type="pmid">16602946</pub-id></citation></ref>
<ref id="B75"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Velazhahan</surname> <given-names>R.</given-names></name> <name><surname>Datta</surname> <given-names>S. K.</given-names></name> <name><surname>Muthukrishnan</surname> <given-names>S.</given-names></name></person-group> (<year>1999</year>). &#x201C;<article-title>The PR-5 family: thaumatin-like proteins</article-title>,&#x201D; in <source><italic>Pathogenesis-Related Proteins in Plants</italic></source>, <role>eds</role> <person-group person-group-type="editor"><name><surname>Datta</surname> <given-names>S. K.</given-names></name> <name><surname>Muthukrishnan</surname> <given-names>S.</given-names></name></person-group> (<publisher-loc>Boca Raton, FL</publisher-loc>: <publisher-name>CRC Press</publisher-name>), <fpage>107</fpage>&#x2013;<lpage>129</lpage>.</citation></ref>
<ref id="B76"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>F.</given-names></name> <name><surname>Yuan</surname> <given-names>S.</given-names></name> <name><surname>Wu</surname> <given-names>W.</given-names></name> <name><surname>Yang</surname> <given-names>Y.</given-names></name> <name><surname>Cui</surname> <given-names>Z.</given-names></name> <name><surname>Wang</surname> <given-names>H.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>TaTLP1 interacts with TaPR1 to contribute to wheat defense responses to leaf rust fungus.</article-title> <source><italic>PLoS Genet.</italic></source> <volume>16</volume>:<issue>e1008713</issue>. <pub-id pub-id-type="doi">10.1371/journal.pgen.1008713</pub-id> <pub-id pub-id-type="pmid">32658889</pub-id></citation></ref>
<ref id="B77"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>X.</given-names></name> <name><surname>Tang</surname> <given-names>C.</given-names></name> <name><surname>Deng</surname> <given-names>L.</given-names></name> <name><surname>Cai</surname> <given-names>G.</given-names></name> <name><surname>Liu</surname> <given-names>X.</given-names></name> <name><surname>Liu</surname> <given-names>B.</given-names></name><etal/></person-group> (<year>2010</year>). <article-title>Characterization of a pathogenesis-related thaumatin-like protein gene TaPR5 from wheat induced by stripe rust fungus.</article-title> <source><italic>Physiol. Plant.</italic></source> <volume>139</volume> <fpage>27</fpage>&#x2013;<lpage>38</lpage>. <pub-id pub-id-type="doi">10.1111/j.1399-3054.2009.01338.x</pub-id> <pub-id pub-id-type="pmid">20059734</pub-id></citation></ref>
<ref id="B78"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yan</surname> <given-names>X.</given-names></name> <name><surname>Qiao</surname> <given-names>H.</given-names></name> <name><surname>Zhang</surname> <given-names>X.</given-names></name> <name><surname>Guo</surname> <given-names>C.</given-names></name> <name><surname>Wang</surname> <given-names>M.</given-names></name> <name><surname>Wang</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2017</year>). <article-title>Analysis of the grape (<italic>Vitis vinifera</italic> L.) thaumatin-like protein (TLP) gene family and demonstration that TLP29 contributes to disease resistance.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>7</volume>:<issue>4269</issue>. <pub-id pub-id-type="doi">10.1038/s41598-017-04105-w</pub-id> <pub-id pub-id-type="pmid">28655869</pub-id></citation></ref>
<ref id="B79"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname> <given-names>Y. W.</given-names></name> <name><surname>Lai</surname> <given-names>K. N.</given-names></name> <name><surname>Tai</surname> <given-names>P. Y.</given-names></name> <name><surname>Li</surname> <given-names>W. H.</given-names></name></person-group> (<year>1999</year>). <article-title>Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages.</article-title> <source><italic>J. Mol. Evol.</italic></source> <volume>48</volume> <fpage>597</fpage>&#x2013;<lpage>604</lpage>. <pub-id pub-id-type="doi">10.1007/PL00006502</pub-id> <pub-id pub-id-type="pmid">10198125</pub-id></citation></ref>
<ref id="B80"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yu</surname> <given-names>C.-S.</given-names></name> <name><surname>Chen</surname> <given-names>Y.-C.</given-names></name> <name><surname>Lu</surname> <given-names>C.-H.</given-names></name> <name><surname>Hwang</surname> <given-names>J.-K.</given-names></name></person-group> (<year>2006</year>). <article-title>Prediction of protein subcellular localization.</article-title> <source><italic>Proteins Struct. Funct. Bioinform.</italic></source> <volume>64</volume> <fpage>643</fpage>&#x2013;<lpage>651</lpage>. <pub-id pub-id-type="doi">10.1002/prot.21018</pub-id> <pub-id pub-id-type="pmid">16752418</pub-id></citation></ref>
<ref id="B81"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Yang</surname> <given-names>Y.</given-names></name> <name><surname>Wang</surname> <given-names>C.</given-names></name> <name><surname>Liu</surname> <given-names>M.</given-names></name> <name><surname>Li</surname> <given-names>H.</given-names></name> <name><surname>Fu</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2014</year>). <article-title>Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew.</article-title> <source><italic>BMC Genomics</italic></source> <volume>15</volume>:<issue>898</issue>. <pub-id pub-id-type="doi">10.1186/1471-2164-15-898</pub-id> <pub-id pub-id-type="pmid">25318379</pub-id></citation></ref>
<ref id="B82"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>J.</given-names></name> <name><surname>Wang</surname> <given-names>F.</given-names></name> <name><surname>Liang</surname> <given-names>F.</given-names></name> <name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Ma</surname> <given-names>L.</given-names></name> <name><surname>Wang</surname> <given-names>H.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Functional analysis of a pathogenesis-related thaumatin-like protein gene TaLr35PR5 from wheat induced by leaf rust fungus.</article-title> <source><italic>BMC Plant Biol.</italic></source> <volume>18</volume>:<issue>76</issue>. <pub-id pub-id-type="doi">10.1186/s12870-018-1297-2</pub-id> <pub-id pub-id-type="pmid">29728059</pub-id></citation></ref>
<ref id="B83"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name></person-group> (<year>2005</year>). <article-title>A putative nucleoporin 96 is required for both basal defense and constitutive resistance responses mediated by suppressor of npr1-1, constitutive 1.</article-title> <source><italic>Plant Cell</italic></source> <volume>17</volume> <fpage>1306</fpage>&#x2013;<lpage>1316</lpage>. <pub-id pub-id-type="doi">10.1105/tpc.104.029926</pub-id> <pub-id pub-id-type="pmid">15772285</pub-id></citation></ref>
<ref id="B84"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Liu</surname> <given-names>Z.</given-names></name> <name><surname>Khan</surname> <given-names>A. A.</given-names></name> <name><surname>Lin</surname> <given-names>Q.</given-names></name> <name><surname>Han</surname> <given-names>Y.</given-names></name> <name><surname>Mu</surname> <given-names>P.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Expression partitioning of homeologs and tandem duplications contribute to salt tolerance in wheat (<italic>Triticum aestivum</italic> L.).</article-title> <source><italic>Sci. Rep.</italic></source> <volume>6</volume>:<issue>21476</issue>. <pub-id pub-id-type="doi">10.1038/srep21476</pub-id> <pub-id pub-id-type="pmid">26892368</pub-id></citation></ref>
<ref id="B85"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Shih</surname> <given-names>D. S.</given-names></name></person-group> (<year>2007</year>). <article-title>Isolation of an osmotin-like protein gene from strawberry and analysis of the response of this gene to abiotic stresses.</article-title> <source><italic>J. Plant Physiol.</italic></source> <volume>164</volume> <fpage>68</fpage>&#x2013;<lpage>77</lpage>. <pub-id pub-id-type="doi">10.1016/j.jplph.2006.02.002</pub-id> <pub-id pub-id-type="pmid">16603274</pub-id></citation></ref>
</ref-list>
<fn-group>
<fn id="footnote1">
<label>1</label>
<p><ext-link ext-link-type="uri" xlink:href="http://wheat.pw.usda.gov/ggpages/wgc/98/Intro.htm">http://wheat.pw.usda.gov/ggpages/wgc/98/Intro.htm</ext-link></p></fn>
<fn id="footnote2">
<label>2</label>
<p><ext-link ext-link-type="uri" xlink:href="http://plants.ensembl.org/">http://plants.ensembl.org/</ext-link></p></fn>
<fn id="footnote3">
<label>3</label>
<p><ext-link ext-link-type="uri" xlink:href="http://www.plantbreeding.wur.nl/uk/software_mapinspect.html.2012">http://www.plantbreeding.wur.nl/uk/software_mapinspect.html.2012</ext-link></p></fn>
<fn id="footnote4">
<label>4</label>
<p><ext-link ext-link-type="uri" xlink:href="https://www.ebi.ac.uk/Tools/msa/clustalo">https://www.ebi.ac.uk/Tools/msa/clustalo</ext-link></p></fn>
<fn id="footnote5">
<label>5</label>
<p><ext-link ext-link-type="uri" xlink:href="https://urgi.versailles.inra.fr/files/RNASeqWheat/">https://urgi.versailles.inra.fr/files/RNASeqWheat/</ext-link></p></fn>
</fn-group>
</back>
</article>