<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" "journalpublishing.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" article-type="research-article" dtd-version="2.3" xml:lang="EN">
<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.2023.1290836</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>DNA barcoding and comparative RNA-Seq analysis provide new insights into leaf formation using a novel resource of high-yielding <italic>Epimedium koreanum</italic>
</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>Yang</surname>
<given-names>Jiaxin</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2585274"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
<role content-type="https://credit.niso.org/contributor-roles/formal-analysis/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
</contrib>
<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>Fan</surname>
<given-names>Siqing</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2585284"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/data-curation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Guo</surname>
<given-names>Min</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/611056"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Xie</surname>
<given-names>Zhaoqi</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2585470"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Cheng</surname>
<given-names>Qiqing</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="https://loop.frontiersin.org/people/1591868"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/software/"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Gao</surname>
<given-names>Puxin</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2227359"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Cheng</surname>
<given-names>Chunsong</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1564447"/>
<role content-type="https://credit.niso.org/contributor-roles/investigation/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
<role content-type="https://credit.niso.org/contributor-roles/conceptualization/"/>
<role content-type="https://credit.niso.org/contributor-roles/funding-acquisition/"/>
<role content-type="https://credit.niso.org/contributor-roles/project-administration/"/>
<role content-type="https://credit.niso.org/contributor-roles/resources/"/>
<role content-type="https://credit.niso.org/contributor-roles/supervision/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Lushan Botanical Garden, Chinese Academic of Sciences</institution>, <addr-line>Jiujiang</addr-line>, <country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>School of Pharmacy, Hubei University of Science and Technology</institution>, <addr-line>Xianning</addr-line>, <country>China</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences</institution>, <addr-line>Beijing</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Svein &#xd8;ivind Solberg, Inland Norway University of Applied Sciences, Norway</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Yun-peng Du, Beijing Academy of Agricultural and Forestry Sciences, China</p>
<p>Adil Hussain, Abdul Wali Khan University, Pakistan</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Chunsong Cheng, <email xlink:href="mailto:chengcs@lsbg.cn">chengcs@lsbg.cn</email>; Puxin Gao, <email xlink:href="mailto:gaopx@lsbg.cn">gaopx@lsbg.cn</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors have contributed equally to this work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>18</day>
<month>12</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="collection">
<year>2023</year>
</pub-date>
<volume>14</volume>
<elocation-id>1290836</elocation-id>
<history>
<date date-type="received">
<day>08</day>
<month>09</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>20</day>
<month>11</month>
<year>2023</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2023 Yang, Fan, Guo, Xie, Cheng, Gao and Cheng</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Yang, Fan, Guo, Xie, Cheng, Gao and Cheng</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>
<italic>Epimedium koreanum</italic> Nakai, a well-known traditional Chinese medicinal herb, has been widely used to treat osteoporosis and sexual dysfunction for thousands of years. However, due to the decreasing population of East Asian natural resources, yearly output of Epimedium crude herb has been in low supply year by year. In this study, an unusual variety of <italic>E. koreanum</italic> was discovered in Dunhua, Jilin Province, the northernmost area where this variety was found containing 6 individuals, with three branches that had 27 leaflets, which is much more than the typical leaflet number of 9. Firstly, the novel <italic>E. koreanum</italic> varety was identified using DNA barcodes. Then, 1171 differentially expressed genes (DEGs) were discovered through parallel RNA-seq analysis between the newly discovered variety and wild type (WT) <italic>E. koreanum</italic> plant. Furthermore, the results of bioinformatics investigation revealed that 914 positively and 619 negatively correlated genes associated with the number of leaflets. Additionally, based on RNA-Seq and qRT-PCR analysis, two homologous hub <italic>TCP</italic> genes, which were commonly implicated in plant leaf development, and shown to be up regulated and down regulated in the discovered newly variety, respectively. Thus, our study discovered a novel wild resource for leaf yield rewarding medicinal <italic>Epimedium</italic> plant breeding, provided insights into the relationship between plant compound leaf formation and gene expression of <italic>TCPs</italic> transcription factors and other gene candidates, providing bases for creating high yield cultivated <italic>Epimedium</italic> variety by using further molecular selection and breeding techniques in the future.</p>
</abstract>
<kwd-group>
<kwd>
<italic>Epimedium</italic>
</kwd>
<kwd>DEGs</kwd>
<kwd>compound leaf</kwd>
<kwd>
<italic>EkTCP</italic>
</kwd>
<kwd>plant selection</kwd>
<kwd>leaf yield</kwd>
</kwd-group>    <contract-num rid="cn001">82260746</contract-num>    <contract-sponsor id="cn001">National Natural Science Foundation of China<named-content content-type="fundref-id">10.13039/501100001809</named-content>
</contract-sponsor>
<counts>
<fig-count count="7"/>
<table-count count="1"/>
<equation-count count="0"/>
<ref-count count="66"/>
<page-count count="14"/>
<word-count count="6844"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Plant Breeding</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<label>1</label>
<title>Introduction</title>
<p>
<italic>Epimedium</italic> is the largest herbaceous genus in berberidaceae family (<xref ref-type="bibr" rid="B63">Zhang et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B62">Zhang et&#xa0;al., 2022</xref>). Herbal <italic>Epimedium</italic>, first described in the <italic>Shen Nong Herbal Classics</italic>, is a prominent traditional Chinese medicinal plant, that has been widely used to treat osteoporosis and sexual dysfunction for thousands of years. There are currently 62 <italic>Epimedium</italic> species, 52 species are indigenous to China (<xref ref-type="bibr" rid="B62">Zhang et&#xa0;al., 2022</xref>). The published papers showed that Epimedium leaves contain a large number of flavonoid chemical components, which provides beneficial properties including anti-cancer effects and the treatment of cardiovascular diseases, rheumatoid arthritis, osteoporosis, and immune enhancement (<xref ref-type="bibr" rid="B36">Li et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B41">Ma et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B17">Jiang et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B16">Indran et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B18">Jiao et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B38">Liu et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B66">Zhu et&#xa0;al., 2021</xref>). In the <italic>Pharmacopoeia of the People&#x2019;s Republic of China</italic> (<italic>Ch. P</italic>), total flavonoids and flavonoid glycoside quantitation serve as indicators of the herbal Epimedium quality. Additionally, polysaccharides, another medicinal component of Epimedium, have antiviral, anti-aging, and immune-regulating activities.</p>
<p>The majority of Epimedium research focused on the therapeutic benefit and chemical potential of its metabolites. However, there have been few studies that dived into botany and plant physiology, specifically the molecular processes that regulate the growth and development of herbal Epimedium. Among the statutory 5 medicinal <italic>Epimedium</italic> species recorded in the <italic>Ch. P</italic>, <italic>Epimedium koreanum</italic> is one of the species with a large amount of wild resources across in the two northeastern provinces of China, Jilin and Liaoning provinces. It primarily spreads in Eastern Asia, with notable distribution in China, Korea, and Japan (<xref ref-type="bibr" rid="B32">Lee et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B46">Qian et&#xa0;al., 2023</xref>). While the published papers on <italic>E. koreanum</italic> have mainly focused on recourse protection and sustainable utilization, including resource collection, cultivation, geographical distribution characteristics, and medical and pharmaceutical applications of its metabolites (<xref ref-type="bibr" rid="B65">Zhong et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B64">Zhang et&#xa0;al., 2020</xref>), and there have been few investigations on its plant physiology and molecular characteristics. (<xref ref-type="bibr" rid="B32">Lee et&#xa0;al., 2016</xref>). <italic>E. koreanum</italic> has been in low supply in the Chinese herbal medicine market in recent years due to the depletion of natural resources across East Asia, and its price has been rising year by year. With the foreseeable rising market demands, the crude herb of wild <italic>E. koreanum</italic> supplies are depleting, and cultivated <italic>E. koreanum</italic> will become the most important raw materials in the primary market. So, it is critical to use molecular techniques to create and select new <italic>E. koreanum</italic> varieties.</p>
<p>The principal photosynthetic organs of flowering plants, with great diversity in number, shape, and structure. Leaves are scientifical ciencclassified into two categories based on the number of leaflets and the structure of the leaf: simple leaves and complex leaves with many leaflets. A compound leaf, distinguished by its potential to take on many forms such as pinnate and palmate compound leaves, is made up of numerous discontinuous leaf units attached to the rachis and petiole, as opposed to a simple leaf, which is a single unit (<xref ref-type="bibr" rid="B25">Kim et&#xa0;al., 2003</xref>). Each leaflet in a complex leaf provides the same photosynthetic function as a simple leaf. From a functional aspect, each leaflet fulfills the same job as a simple leaf; hence, the development of complex leaves may boost plants&#x2019; capacity for photosynthetic energy generation and plant survival rate (<xref ref-type="bibr" rid="B31">Laura et&#xa0;al., 2010</xref>).</p>
<p>At present, the mechanism of compound leaf development and formation is not well understood. Leaf shape develops from the apical meristem (SAM) of the plant, while the leaf primordium cells develop from the flanks of SAM. Leaf development must arises in three distinct and overlapping stages: The first stage is leaf initiation, in which the leaf primordium differentiates from the flank of SAM; this is followed by primary morphogenesis (PM), in which leaf margin structures such as blade, serrate, and lobes begin to form; and finally, secondary morphogenesis (SM), which determines the final size and shape of the leaf (<xref ref-type="bibr" rid="B9">Dengler and Tsukaya, 2001</xref>; <xref ref-type="bibr" rid="B1">Bar and Ori, 2015</xref>). Leaf development is regulated by transcription factors and phytohormone networks. One of the essential genes involved in regulating leaf growth is the plant specific transcription factors <italic>TEOSINTE BRANCHED1 CYCLOIDEA PROLIFERATING CELL FACTOR</italic> (<italic>TCP</italic>). Various <italic>TCP</italic> transcription factors have been identified as critical modulators of leaf architecture. For instance, in tomato (<italic>Solanum lycopersicum</italic>), the <italic>TCP</italic> gene family member <italic>LANCEOLATE</italic> (<italic>LA</italic>) was showed exhibiting the premature leaf differentiation in the gain-of-function mutant <italic>La-2</italic>, resulting in a single-leaf pattern. Conversely, the loss of function mutant <italic>la-6</italic> displayed highly fragmented leaf margin shape, indicating the involvement of <italic>LA</italic> in leaf development (<xref ref-type="bibr" rid="B44">Ori et&#xa0;al., 2007</xref>). In <italic>Arabidopsis</italic>, the microRNA <italic>miR319</italic> was found to down-regulate the expression of <italic>TCP</italic> gene family members, thereby influencing leaf morphogenesis (<xref ref-type="bibr" rid="B27">Koyama et&#xa0;al., 2017</xref>). Similarly, <italic>TCP13</italic> was showed to regulate leaf and root growth in response to drought conditions in <italic>Arabidopsis</italic> (<xref ref-type="bibr" rid="B56">Urano et&#xa0;al., 2022</xref>). Furthermore, in lettuce (<italic>Lactuca sativa L.</italic>), the <italic>LsAP2</italic> gene promoted the leaf division by inhibiting <italic>TCP</italic> transcription factor activity, emphasizing the significance of <italic>TCPs</italic> in leaf development across different plant species (<xref ref-type="bibr" rid="B40">Luo et&#xa0;al., 2021</xref>). In addition, aside from the compound leaf plant tomato, there have few number of studies investigating compound leaf development in other plant species such as medicago (<italic>Medicago truncatula</italic>) and pea (<italic>Pisum sativum</italic>). In medicago, the <italic>PINNATE LIKE PENTAFOLIATA1</italic> (<italic>PINNA1</italic>) gene was identified as a key regulator of terminal leaflet morphogenesis. It works by inhibiting the expression of the <italic>FLORICAULA</italic>/<italic>LFY</italic> homologous gene, <italic>SINGLE LEAFLET1</italic> (<italic>SGL1</italic>), thereby suppressing the formation of lateral leaflets (<xref ref-type="bibr" rid="B14">He et&#xa0;al., 2020</xref>). Similarly, in peas, research focused on the <italic>afila</italic> (<italic>af</italic>) mutant, which exhibits increased leaf complexity. This increase in leaf complexity is accompanied by elevated expression of the <italic>UNIFOLIATA</italic> (<italic>UNI</italic>) gene. Further investigations involving the double mutant <italic>af tendril</italic> (<italic>tl</italic>) also revealed a synergistic effect, with heightened <italic>UNI</italic> expression suggesting that <italic>AF</italic> and <italic>TL</italic> jointly inhibit leaflet formation (<xref ref-type="bibr" rid="B42">Mishra et&#xa0;al., 2009</xref>; <xref ref-type="bibr" rid="B8">Demason et&#xa0;al., 2013</xref>). While there has been considerable research on compound leaf development in tomato, pea, and medicago, studies investigating the mechanism of compound leaf development in medicinal plants are currently lacking for scientific community. This knowledge gap is especially concerning in light of the scientific and practical consequences for medicinal or commercial plants that relys on complex leaves as harvesting and therapeutic components. Understanding the development and regulation of leaflets in medicinal plant species holds immense potential for enhancing their cultivation, yield, and medicinal properties. Therefore, imperious demands are expected to investigate compound leaf development in medicinal plants and uncover the underlying molecular mechanisms.</p>
<p>During extensive field investigations and resource collection encompassing various species of <italic>Epimedium</italic>, our research team made an intriguing discovery that the presence of a distinct <italic>Epimedium</italic> plant displayed remarkable characteristics in the primary growth region of <italic>E. koreanum</italic> in northeast China. This unique wild resource exhibited an unprecedented number of leaflets, ranging from 11 to 27, surpassing the typical 9 leaflets observed in <italic>E. koreanum</italic>. To unravel the taxonomic implications associated with this finding, we rigorously employed DNA barcode analysis and constructed an evolutionary tree, aiming to ascertain whether this variant represented a new species of <italic>E. koreanum</italic>. Subsequently, we performed comprehensive investigations on this &#x201c;super <italic>Epimedium</italic>&#x201d; plant. Fresh leaf tissues were carefully sampled and subjected to global RNA sequencing (RNA-Seq) and qRT-PCR analysis, allowing us to delve into the intricate molecular mechanisms underlying its exceptional leaf development. Through rigorous analysis of differential gene expression (DEGs) and comparison of gene expression patterns, we gained valuable insights into the critical signaling pathways involved in leaf development. By integrating these findings with important molecular pathways, we aimed to gain a holistic understanding of compound leaf morphogenesis in <italic>E. koreanum</italic>. Ultimately, our study endeavored to improve our understanding of compound leaf morphogenesis in <italic>E. koreanum</italic> while also opening up novel prospects for future selection and breeding.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<label>2</label>
<title>Materials and methods</title>
<sec id="s2_1">
<label>2.1</label>
<title>Sample collection</title>
<p>The material used in this study were <italic>E.koreanum</italic> and the discovered newly variation. The newly variation named <italic>E. koreanum</italic> var. <italic>polyphylla</italic> CS Cheng (EKP) in this study collected from in Dunhua City Jilin Province (E: 128.0369, N: 43.1156, A: 670) and ex-situ cultivated in the E115&#xb0;59&#x2032;, N29&#xb0;51&#x2032; at Lushan Botanical Garden.</p>
</sec>
<sec id="s2_2">
<label>2.2</label>
<title>Sequence mining and primer design</title>
<p>The nucleic acid sequences of each species within the genus <italic>Epimedium</italic> were downloaded from the NCBI website (<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov">https://www.ncbi.nlm.nih.gov</ext-link>) by searching with &#x201c; &#x2018;<italic>Epimedium</italic>&#x2019; [organism] and &#x2018;<italic>matK</italic>&#x2019; [All fileds] &#x201c;. The <italic>ITS</italic>, <italic>rbcL</italic>, and <italic>trnL-trnF</italic> sequences were also searched and downloaded in a similar manner. Save the downloaded sequences with Geneious primer 2021 software (<xref ref-type="bibr" rid="B20">Kearse et&#xa0;al., 2012</xref>) for the subsequent steps of nucleic acid sequence SNP analysis. The <italic>matK</italic> sequence (GenBank: AB069837.1) of <italic>E. koreanum</italic> species was used as the reference sequence and Primer premier 5.0 was used for primer design (<xref ref-type="bibr" rid="B35">Li et&#xa0;al., 2009</xref>). The primer sequences were designed as:</p>
<p>
<italic>matK</italic> forward primer (FmatK): 5&#x2019;-TATGACAATAAATCCAGTTC-3&#x2019;</p>
<p>
<italic>matK</italic> reverse primer (RmatK): 5&#x2019;-ATGCCCCGATACGTTACAAA-3&#x2019;</p>
</sec>
<sec id="s2_3">
<label>2.3</label>
<title>DNA extraction and DNA sequencing</title>
<p>Genomic DNA from leaves was isolated using the standard Cetyltrimethyl ammonium bromid (CTAB) extraction protocol (<xref ref-type="bibr" rid="B15">Helliwell et&#xa0;al., 2016</xref>). The targeted sequences were amplified with specific primers. The standard 50 &#x3bc;L PCR reaction mixture contained 25 &#x3bc;L of 2 &#xd7; PrimeSTAR<sup>&#xae;</sup> Max DNA Polymerase (Takara, Code NO. R045A) and 10 ng of template DNA, 0.2 &#x3bc;M of each primer. The samples were amplified using a Verit 96- Well Fast Thermal Cycler (Applied Biosystems, Foster City, CA, USA) under the following conditions: initial denaturation at 94 &#xb0;C for 5 min, followed by 30 cycles of denaturation at 98 &#xb0;C for 10 s, annealing at 54 &#xb0;C for 10 s, extension at 72 &#xb0;C for 30 s, and a final elongation step at 72 &#xb0;C for 7 min. The PCR products were confirmed by 1.0% agarose gel electrophoresis in 1 &#xd7; TAE buffer to detect whether the target sequences were cloned successfully. The amplicons were purified with an TaKaRaMinBEST Agarose Gel DNA Extraction Kit Ver.4.0 (Takara, Code No.9762) and quantified with a NaoDrop 2000 spectrophptometer (Thermo Fisher Scientific) (<xref ref-type="bibr" rid="B37">Lin et&#xa0;al., 2021</xref>). And then the target fragments were sent to BGI (Wuhan, China) for bidirectional sequencing.</p>
</sec>
<sec id="s2_4">
<label>2.4</label>
<title>Sequence analysis</title>
<p>To discover the SNP of sequences, sequenced sequences and <italic>matK</italic> sequences downloaded from NCBI were subjected to multiple sequence alignments through Geneious primer 2021 software with default settings. Polymorphic locis were counted after multiple alignment for different species. In the <italic>Geneious</italic> software, the head and tail of the aligned <italic>matK</italic> sequences were cut off while removing the gaps in different species, respectively. Then, intraspecific genetic distances were calculated as SNP%. Six species in the <italic>Epimedium</italic> genus were randomly selected, and all <italic>matK</italic> sequences of each species were randomly sampled with put-back six times for sequence alignments, and then the calculated SNP% was used as the interspecific genetic distance. The <italic>ITS</italic>, <italic>rbcL</italic>, and t<italic>rnL-trnF</italic> sequences were also handled as described above.</p>
</sec>
<sec id="s2_5">
<label>2.5</label>
<title>Phylogenetic analysis</title>
<p>Test sequences from the collected samples and <italic>matK</italic> sequences downloaded from NCBI for all species of the <italic>Epimedium</italic> genus were used for multiple sequence alignments through MEGA-X (<xref ref-type="bibr" rid="B28">Kumar et&#xa0;al., 2018</xref>) with the default setting. Then, they were performed cutting the head and tail, as well as aligning the gaps in the sequence. To compare the evolutionary relationships, the results of the above alignments and processing were used to construct the phylogenetic tree using MEGA-X with Maximum Likelihood (ML) method. The phylogenetic tree was then visualized by EVOLVIEW. (<ext-link ext-link-type="uri" xlink:href="https://www.evolgenius.info/evolview/#login">https://www.evolgenius.info/evolview/#login</ext-link>).</p>
<p>To build phylogenetic tree of <italic>TCP</italic> proteins, the <italic>TCP</italic> protein sequences were first aligned with MAFFT (Version 7.037b) (model: &#x201c;BLOSUM62&#x201d;, strategy: &#x201c;L-INS-i&#x201d;) (<xref ref-type="bibr" rid="B19">Katoh and Standley, 2013</xref>), then refined conserved sequences from the alignments by Gblocks (Version 0.91b) (Maximum number of contiguous noncom served positions: 32000, Minimum length of a block: 2, Allowed gap positions: all) (<xref ref-type="bibr" rid="B2">Castresana, 2000</xref>). The neighbor-joining phylogenetic tree was finally generated with Mega 6 (<xref ref-type="bibr" rid="B54">Tamura et&#xa0;al., 2013</xref>).</p>
</sec>
<sec id="s2_6">
<label>2.6</label>
<title>Geographic analysis</title>
<p>According to the origin information of different species of <italic>Epimedium</italic> genus (<ext-link ext-link-type="uri" xlink:href="http://www.iplant.cn/">http://www.iplant.cn/</ext-link>, <ext-link ext-link-type="uri" xlink:href="http://www.plantsoftheworldonline.org/">http://www.plantsoftheworldonline.org/</ext-link>), the latitude and longitude of origins were also found and recorded by Google Earth. The locations were projected to the provincial boundary map of China depended on the latitude and longitude data by ArcGIS10 software to observe and analysis the distribution of different groups.</p>
</sec>
<sec id="s2_7">
<label>2.7</label>
<title>mRNA sequencing</title>
<p>The newly developed leaves of <italic>E.koreanum</italic> in the rainy season of August in Jilin Province were collected for molecular sequencing analyses. The two groups of <italic>E. koreanum</italic> with significant differences in leaf shape and number of leaflets of compound leaves were named variety and normal. And, each sample was blended with several leaflets from the same biological source, and at least three biological duplicate samples were chosen for each group in this investigation. All samples were powdered by liquid nitrogen quick-freezing and then RNA was extracted. Nanodrop 2000 (ThermoFisher) was used for purity and concentration detection of the extracted RNA, RNA integrity was detected by agarose gel electrophoresis, and Agilent 2100 was used to determine the RIN value. Four samples were send to BGI Genomics Co., Ltd. (East Lake Development Area, Wuhan, China) for library preparation and RNA sequencing. Using the BGISEQ-500 sequencing platform, sequencing data quality control included sequencing data statistics, original data statistics and quality control data statistics.</p>
</sec>
<sec id="s2_8">
<label>2.8</label>
<title>Transcriptome data analysis</title>
<p>Data filtering: The raw data obtained from sequencing was filtered using the filtering software fastp (<xref ref-type="bibr" rid="B4">Chen et&#xa0;al., 2018</xref>) to remove reads containing adapters (adapter contamination), reads with unknown base N content greater than 5%, and low-quality reads (reads with a quality value below 15 that account for more than 20% of the total bases in the read). <italic>De novo</italic> assembly and quality assessment: Clean reads were assembled <italic>de novo</italic> using Trinity (<xref ref-type="bibr" rid="B11">Grabherr et&#xa0;al., 2011</xref>), and their assembly quality was evaluated using BUSCO. Reference gene alignment: Clean data was aligned to reference gene sequences using Bowtie 2 (v2.2.5) (<xref ref-type="bibr" rid="B30">Langmead and Salzberg, 2012</xref>)software, and gene and transcript expression levels were calculated using RSEM software (<xref ref-type="bibr" rid="B34">Li and Dewey, 2011</xref>). CDS prediction: Candidate coding regions within transcripts were identified using Transdecode software (<xref ref-type="bibr" rid="B24">Kim et&#xa0;al., 2015</xref>), and BLASTed against SwissProt and searched for Pfam protein homologous sequences were using the Hmmscan to predict coding regions. Gene annotation: Transcripts were annotated with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG). WGCNA analysis: Gene co-expression networks were analyzed using WGCNA (v1.48). differentially expressed genes: Group difference gene analysis was performed using DESeq 2 (<xref ref-type="bibr" rid="B39">Love et&#xa0;al., 2014</xref>), with the condition that Fold Change &#x2265; 1 and padj value (after multiple correction) was less than 0.05. Based on GO annotation results and official classification, differentially expressed genes were classified functionally, and GO enrichment analysis was performed using the clusterProfile package (<xref ref-type="bibr" rid="B60">Wu et&#xa0;al., 2021</xref>). A threshold of qvalue &#x2264; 0.05 was used in where a definition of significant enrichment in candidate genes was met.</p>
</sec>
<sec id="s2_9">
<label>2.9</label>
<title>Validation of differential gene expression by qRT-PCR analysis</title>
<p>RNA extraction and cDNA synthesis: Total RNA was extracted from the frozen leaf samples with the MiniBEST Plant RNA Extration Kit (TaKaRa, China). The NanoDrop ND1000 spectrophotometer (Thermo, USA) was used to calculate the RNA concentration and assess purity. The RNA samples with a 260/280 nm absorbance ratio of 1.8&#x2013;2.0 were retained for further analyses. The RNA integrity was evaluated by 1% agarose gel electrophoresis. The HiScript@III RT SuperMix for qPCR (Vazyme) was used to synthesize cDNA.The qRT-PCR assay was completed with SYBR qPCR Master Mix (Vazyme) and The LightCycle 480 Instrument II(Roche). The reaction solution consisted of 5 &#x3bc;L SYBR qPCR Master Mix (Vazyme), 4 &#x3bc;L cDNA (100 ng), 0.5 &#x3bc;L 10 &#xb5;M forward primer, 0.5 &#x3bc;L 10 &#xb5;M reverse primer for a final volume of 10 &#x3bc;L (<xref ref-type="table" rid="T1"><bold>Table 1</bold></xref>). The amplification conditions were as follows: 95&#xb0;C for 3min s; 40 cycles of 95&#xb0;C for 10 s, 58&#xb0;C for 10 s, and 72&#xb0;C for 25 s, followed by a melting curve analysis from 60 to 95&#xb0;C. The gene expression levels for each sample were determined based on three replicates.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Primer sequences used in this study.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Primer name</th>
<th valign="top" align="center">Primer sequence</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">
<italic>EkTCP14</italic>-QF<break/>
<italic>EkTCP14</italic>-QR<break/>
<italic>EkTCP9-</italic>QF<break/>
<italic>EkTCP9</italic>-QR<break/>
<italic>EkACT2-</italic>QF<break/>
<italic>EkACT2</italic>-QR<break/>
<italic>EkSERK1</italic>-QF<break/>
<italic>EkSERK1</italic>-QR<break/>
<italic>EkACC2</italic>-QF<break/>
<italic>EkACC2</italic>-QR<break/>
<italic>EkSUS4</italic>-QF<break/>
<italic>EkSUS4</italic>-QR<break/>
<italic>EkSPL1</italic>-QF<break/>
<italic>EkSPL1</italic>-QR<break/>
<italic>EkARP8</italic>-QF<break/>
<italic>EkARP8</italic>-QR<break/>
<italic>EkCDKE-1</italic>-QF<break/>
<italic>EkCDKE-1</italic>-QR</td>
<td valign="top" align="left">5&#x2019;-ATGGGAGATACCAAACCAAGTGAAA-3&#x2019;<break/>5&#x2019;-TCCACCTTTGTGTGTCTGTCCT-3&#x2019;<break/>5&#x2019;-CCGATGTGGGCGATGGT-3&#x2019;<break/>5&#x2019;-GAACTTGAATAGCGTTTGCCAT-3&#x2019;<break/>5'-GCCATTCAGGCTGTTCTTTC-3'<break/>5'-GGTAAGATCGCGACCTGCTA-3'<break/>5'-CACTTTTCCTATTTGCTGTCGC -3'<break/>5'-TTTACCAAACCCTCCTCTACCC -3'<break/>5&#x2019;-GAGACGAATCATACCGCTCACC-3&#x2019;<break/>5&#x2019;-GAGCGAAGAGCCGAACCTAC-3&#x2019;<break/>5&#x2019;-GCTTTCATTCCCTTTCCCGT-3&#x2019;<break/>5&#x2019;-AGAAGAGAGACTAATTCGTTGCG-3&#x2019;<break/>5&#x2019;-TGGATTTCTGGGGGCATAG-3&#x2019;<break/>5&#x2019;-CCAATAAACCAAACCAAGCCTT-3&#x2019;<break/>5&#x2019;-TTGGGATACTATTGTTTTCGCC-3&#x2019;<break/>5&#x2019;-CGAGGCATATTTACTCCAACCA-3&#x2019;<break/>5&#x2019;-ATCTTCTACCCGCCCTACTTTT-3&#x2019;<break/>5&#x2019;-GCCTGTTGGGATTGTTGTTAGT-3&#x2019;</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s2_10">
<label>2.10</label>
<title>Statistical analysis</title>
<p>Graphpad Prism 7 software was used to analyze the data. All numerical values were presented as mean &#xb1; SEM and the sequence type was indicated in the legends. Statistically significant differences between inter- and intraspecific distance were determined by pair using t-test, with <italic>p</italic> values &lt; 0.05. The three-dimensional structure of TCP proteins were builtin SWISS-MODEL (<ext-link ext-link-type="uri" xlink:href="https://swissmodel.expasy.org">https://swissmodel.expasy.org</ext-link>) (<xref ref-type="bibr" rid="B59">Waterhouse et&#xa0;al., 2018</xref>).</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<label>3</label>
<title>Results</title>
<sec id="s3_1">
<label>3.1</label>
<title>Distinctive resources discovered in the wild population of <italic>Epimedium koreanum</italic>
</title>
<p>Referring to the records of plant specimens collected in China mainland. The sample collection of resources of <italic>E. koreanum</italic> was implemented in August 2021, covering the whole areas along the Yalu River in Jilin and Liaoning provinces (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). A distinctive wild population of <italic>Epimedium</italic> was discovered in Dunhua City Jilin Province (E: 128.0369, N: 43.1156, A: 670). The decovered newly resource contains 6 individuals which grow mixed with ordinary <italic>E. koreanum</italic> under the same masson pine forest. It was hard to tell whether a newly discovered exceptional resource belongs to a budding mutation or a new species on the spot. Its reproductive organs were not appreciably different from those of the typical <italic>E. koreanum</italic> (<xref ref-type="fig" rid="f1"><bold>Figures 1C, D</bold></xref>). The number of their leaves generally exceeds 9, and reaching a maximum of 27, its flower stem often has more than 1 biternate leaf, which is a significant feature of this population (<xref ref-type="fig" rid="f1">
<bold>Figures&#xa0;1B, E&#x2013;G</bold>
</xref>). In details, this wild <italic>Epimedium</italic> is also a perennial herb, with 20-45 cm tall, rhizome creeping, triternate leaves, 11-27 foliolate, leaflets ovate, abaxially pallid but adaxially dark green, 6-16 &#xd7; 4-12 cm, papery, glabrous, base deeply cordate with usually round lobes, margin minutely serrate, apex acute or acuminate. Flowering stem with 2-3 biternate leaf. Simple raceme inflorescence 12-17 cm with 6-16 flowered, glabrous. Pedicel 1-2 cm, flowers yellowish-white, 2-5 cm in diam. Outer sepals reddish or pale yellow, 5-8 mm, inner sepals narrowly ovate to lanceolate and apically acute. Petals nearly twice longer than the inner sepals, spurs slender, elongate and tapering subulate, 1-2 cm. The stamens ca 6.5 mm, anther ca 5 mm, filaments ca 1.5 mm,pistil ca 8 mm, ovary ca 5 mm, capsules 6-12 mm long, and 2-4 mm broad. Seeds usually 5-7. Fl. May, fr. May. Based on the phenotype of the newly resource with strong biomass advantage and the identification of medicinal plant taxonomy by expert Dr. Cheng Chung, we suspected that this is a variety of <italic>E. koreanum</italic>. So, we tentatively named the distinctive resource with <italic>E. koreanum</italic> var. <italic>polyphylla</italic> CS Cheng (EKP) in this study. This exceptional germplasm resource was grown ex-situ at the Lushan Botanical Garden. Moreover, after one year of phenological records performed, most of the phenotypes of complex leaf leaflets may still be maintained (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1E</bold>
</xref>), however the number of leaflets may fluctuate due to soil nutrition or climatic environment.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Discovery of a novel variety of <italic>E koreanum</italic>. <bold>(A)</bold> Red marks represent the areas where the <italic>Epimedium</italic> resources are collected; <bold>(B)</bold> The picture of wild <italic>E koreanum</italic> var. <italic>polyphylla</italic> CS Cheng with 11 blades; <bold>(C)</bold> Specimen of normal <italic>E koreanum</italic>; <bold>(D)</bold> Ex-situ cultivated normal <italic>E koreanum</italic> in Lushan botanical garden; <bold>(E)</bold> Ex-situ cultivated <italic>E koreanum</italic> var. <italic>polyphylla</italic> CS Cheng in Lushan botanical garden; <bold>(F)</bold> Specimen of <italic>E koreanum</italic> var.<italic>polyphylla</italic> CS Cheng with 24 blades; <bold>(G)</bold> Hand drawing of <italic>E koreanum</italic> var. <italic>polyphylla</italic> CS Cheng, the labels (a-e) represent different petiole areas.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1290836-g001.tif"/>
</fig>
</sec>
<sec id="s3_2">
<label>3.2</label>
<title>Molecular identification and phylogenetic tree analysis</title>
<p>The morphological identification of <italic>Epimedium</italic> species and the molecular classification based on DNA barcoding are both challenging (<xref ref-type="bibr" rid="B61">Zhang et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B48">Ren et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B62">Zhang et&#xa0;al., 2022</xref>). However, the application of DNA sequencing and barcoding is undoubtedly crucial for evaluating a new plant resource. In this study, the applied DNA sequences (DNA barcodes) (<xref ref-type="bibr" rid="B57">Vijayan and Tsou, 2010</xref>; <xref ref-type="bibr" rid="B23">Kim et&#xa0;al., 2016</xref>), including <italic>ITS</italic>, <italic>matK</italic>, <italic>rabL</italic> and <italic>trnL-trnF</italic> were evaluated for usability by using the degree of differences in DNA sequences within and between species, also known as intraspecific distance and interspecific distance. According to the DNA sequences statistics of <italic>Epimedium</italic> plants published by NCBI, only <italic>matK</italic> sequence was considered to be suitable for next step of genetic analysis and species identification of the new plant resource, because its interspecific difference was significantly higher than intraspecific difference (P&lt;0.01, N&gt;6) (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>). The other investigated sequences included <italic>ITS</italic>, <italic>rabL</italic>, and<italic>trnL-trnF</italic>, although all showed an average interspecific distance greater than the average intraspecific distance, but the <italic>t-test</italic> result showed no significant differences (P &gt; 0.05, N &gt; 6). Herein, specific primers were designed at the beginning and end of the referenced sequence to maximize the amplification of the <italic>matK</italic> sequence. In order to balance the credibility of public sequences with the longest possible sequence length, the referenced matK sequences were artificially divided into three parts (a, b, and c), differential DNA base count results showed that part b covers the most SNPs in <italic>Epimedium</italic> plants (N &gt; 50, P &lt; 0.001) (<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2B, C</bold>
</xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Scientific screening of commonly used DNA barcodes for assisted identification of Epimedium species. <bold>(A)</bold> The SNP statistics of <italic>Epimedium</italic> genus DNA barcodes within and between species; <bold>(B)</bold> Homologous alignment analysis of matK sequence in the chloroplast genome fingerprint region of Epimedium species, a and c represent the 3 &#x2018;and 5&#x2019; ends of the matK sequence, respectively (prone to sequencing errors or deletions due to primers), and b represents the region with high degree of sequence homology in <italic>Epimedium</italic> genus; <bold>(C)</bold> The distribution and statistics of SNPs in the <italic>matK</italic> sequence of the genus <italic>Epimedium</italic>. Data presented as means &#xb1; SEM (<italic>n</italic> &gt; 6). T-test, **<italic>p</italic> &lt; 0.01 *<italic>p</italic> &lt; 0.05; the dots represent single nucleotide mutation sites, with the first sequence as a reference.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1290836-g002.tif"/>
</fig>
<p>The PCR products were sequenced by Sanger sequencing and verified by positive and negative sequencing (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>). A specific homozygous mutation (T) was generated at site 333, compared to the typical <italic>E. koreanum</italic> population (G) (<xref ref-type="fig" rid="f3">
<bold>Figures 3B, C</bold>
</xref>). Mutations specific to this site appeared to be rare, since all public <italic>matK</italic> sequences showed that only <italic>E. perralderianum</italic> and <italic>E. pinnatum</italic> from the highest latitudes or altitudes (N &gt; 34&#xb0;) have genotype T/T at this site (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3B</bold>
</xref>, <xref ref-type="fig" rid="f4">
<bold>4A</bold>
</xref>, <xref ref-type="supplementary-material" rid="SF1">
<bold>S1</bold>
</xref>). This homozygous SNP site was obviously not created by sequencing errors (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>), and the function of the <italic>matK</italic> gene corresponding to the SNP at this site may be relevant to the evolution of high-latitude plant species. Overall, the confirmation of this discovered SNP verified our idea that this novel resource discovered in wild <italic>E. koreanum</italic> population can be identified as a variety. Although the study of the novel SNP and its kinase function corresponding to the matK gene belongs to an interest scientific issue, as one of the rapidly evolving genes in plant chloroplast genome, matK sequence is often used to assist in the identification of species below plant genera. Therefore, in this study, only the phylogenetic tree of matK sequence was discussed.</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Discovery of mutation sites on the<italic>matK</italic> sequence of <italic>E koreanum</italic> var. <italic>polyphylla</italic> CS Cheng. <bold>(A)</bold> The sequencing electropherogram of the <italic>matK</italic> sequence of <italic>E koreanum</italic> var. <italic>polyphylla</italic> CS Cheng. <bold>(B)</bold> Alignment of <italic>matK</italic> sequences among species of the <italic>Epimedium</italic> genus. <bold>(C)</bold> Alignment of <italic>matK</italic> sequences from <italic>E koreanum</italic>.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1290836-g003.tif"/>
</fig>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Research on the monophyletic origin of the Epimedium genus. <bold>(A)</bold> Phylogenetic tree based on the maximum likelihood method. <bold>(B)</bold> Haplotype parsimony network analysis of the diversity of 52 matK sequences in the Epimedium genus.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1290836-g004.tif"/>
</fig>
<p>As shown in <xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>, the maximum likelihood method based phylogenetic tree was conducted and revealed that the monophyletic origin in <italic>Epimedium</italic> genus, which was consistent with other reports (<xref ref-type="bibr" rid="B63">Zhang et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B12">Guo et&#xa0;al., 2022</xref>). An important group including the <italic>E. koreanum</italic>, which is entirely located at high latitudes and is of particular concern to this study. There were 8 <italic>Epimedium</italic> species in this group, including <italic>E. pinnatum, EKP</italic>, <italic>E. grandiflorum, E. sempervirens, E. diphyllum, E. alpinum, E. pinnatum</italic> and <italic>E. perralderianum.</italic> Furthermore, haplotype parsimony network analysis of matK sequences diversity obtained from sampling 52 sequences (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4B</bold>
</xref>). The network analysis revealed a more distinct genealogical connect among the eight Epimedium species indicated above, which are found in high latitudes all over the world.</p>
</sec>
<sec id="s3_3">
<label>3.3</label>
<title>DEGs analysis for exploring molecular mechanism of leaflets increasing</title>
<p>We investigated the differences in transcription expression levels between <italic>EKP</italic> and <italic>E. koreanum</italic> by second-generation transcriptome sequencing. We used Trimmed Mean of M-values (TMM) to analyze gene transcription levels. The volcano map showed the number of differenced genes between <italic>EKP</italic> and normal <italic>E. koreanum</italic>, and showed significantly up-regulated, down-regulated, and non-significant genes in different colors (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>). The genes that were considerably up-regulated and down-regulated in <italic>EKP</italic> were statistically analyzed in a bar chart, and it was found that 387 genes were significantly up-regulated and 784 genes were significantly down-regulated when compared to the typical <italic>E. koreanum</italic> (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5C</bold>
</xref>). Table was used to show DEGs in this study (<xref ref-type="supplementary-material" rid="SF3">
<bold>Table S1</bold>
</xref>). With these transcripts, we then performed GO enrichment analysis, and we chose the top 10 modules to present (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5B</bold>
</xref>). It was discovered that DEGs were primarily enriched in the development of gametophytes, embryo sacs, flavonoid biosynthetic pathways, and flavonoid metabolic pathways. The majority of the genes involved in the differentiation and proliferation of leaf primordium cells were associated with gametophyte and embryo sac development. The involvement of plant hormones such as auxin and ethylene is widely regarded as important roles in the synergistic regulation of gametophyte and embryo sac development. So these findings provided new insights into <italic>E. koreanum</italic> leaf growth and flavonoid metabolism.</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>The differences in transcription expression levels between <italic>E koreanum</italic> var. <italic>polyphylla</italic> CS Cheng and <italic>E koreanum</italic>. <bold>(A)</bold> The volcano plots. <bold>(B)</bold> The number of DEGs. <bold>(C)</bold> GO enrichment analysis of DEGs.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1290836-g005.tif"/>
</fig>
</sec>
<sec id="s3_4">
<label>3.4</label>
<title>Weighted gene co-expression network analysis for discovery of leaf development related genes</title>
<p>In order to identify the DEGs related to leaf development in <italic>E. koreanum</italic>, we further analyzed leaf development as a trait by WGCNA (<xref ref-type="bibr" rid="B29">Langfelder and Horvath, 2008</xref>). Twenty-one modules were discovered and colored differently. The twenty-one modules&#x2019; gene counted ranged from 120 to 3154 (<xref ref-type="fig" rid="f6">
<bold>Figures&#xa0;6A, C</bold>
</xref>). In this research, we focused on the two main modules. The pink module involved 914transcripts, was positively correlated with leaf development. The green yellow module involved 619 transcripts were negatively correlated with leaf development (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6B</bold>
</xref>). Thus, these results provided a further understanding of leaf development of <italic>E. koreanum</italic>.</p>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>WGCNA analysis of genes related to leaf biomass in <italic>E koreanum</italic>. <bold>(A)</bold> Clustering dendrogram of genes. Similarity is based on topological overlap, with module colors assigned. The 21 co-expression modules are displayed in different colors. <bold>(B)</bold> Correlation between the 21 modules. <bold>(C)</bold> Member count in the 21 modules.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1290836-g006.tif"/>
</fig>
</sec>
<sec id="s3_5">
<label>3.5</label>
<title>Identification of hub genes regulate to the leaf development in <italic>E. koreanum</italic>
</title>
<p>We performed a visual network analysis of these two modules, identified the top 30 most reliable nodes for visualization, and discovered that these hub genes were involved in leaf development (<xref ref-type="fig" rid="f7">
<bold>Figures&#xa0;7A, B</bold>
</xref>). Because no whole genome data for <italic>E. koreanum</italic> is now publicly available, we used homologous alignment to annotate these genes and discovered <italic>TRINITY_DN4142_c0_g1_i1</italic>, a <italic>TCP14</italic> transcription factor homologous gene in green yellow module, which has previously been reported to inhibit cell proliferation in leaf tissues (<xref ref-type="bibr" rid="B21">Kieffer et&#xa0;al., 2011</xref>). Besides, we also found other genes may involve in regulating leaf development, such as <italic>SERK1</italic> in pink module, <italic>SPL1</italic>, <italic>ARP8</italic> and <italic>SUS4</italic> in green yellow module. Although the homologous genes of these genes in other species have rarely been reported to regulate leaf development in other species, they may be involved in leaf development in <italic>Epimedium</italic>. The expression levels of these genes were shown in <xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7C</bold>
</xref>.</p>
<fig id="f7" position="float">
<label>Figure&#xa0;7</label>
<caption>
<p>Visual analysis of modules and expression of hub gene transcripts. <bold>(A)</bold> Hub genes in the pink module. <bold>(B)</bold> Hub genes in the greenyellow module; <bold>(C)</bold> Transcript levels of part hub genes determined by RNA-seq. TMM, Trimmed Mean of M-values; <bold>(D)</bold> Validation of differential gene expressions by qRT-PCR analysis. T-test, **<italic>p</italic> &lt; 0.01 *<italic>p</italic> &lt; 0.05.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1290836-g007.tif"/>
</fig>
<p>Based on the visual network&#x2019;s cues, we used the <italic>TCP</italic> conserved&#xa0;domain homologous comparison method to identify potential <italic>TCP</italic> transcription factors from our transcript data and demonstrated their expression levels (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7C</bold>
</xref>). The transcription of <italic>TRINITY_DN4142_c0_g1_i1</italic> was found to be lower in <italic>E. koreanum</italic> var. <italic>polyphylla</italic> CS Cheng than in the typical <italic>E. koreanum</italic>, the decrease of <italic>EkTCP14</italic> expression may promote the proliferation of cells and thus increase the number of leaves (<xref ref-type="bibr" rid="B21">Kieffer et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B3">Challa et&#xa0;al., 2021</xref>) (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7C</bold>
</xref>). Additionally, we discovered another <italic>TCP9</italic> similar gene, <italic>TRINITY_DN3273_c2_g1_i2</italic>, which is a member of the class I <italic>TCP</italic> family and whose transcripts were up-regulated in <italic>E. koreanum</italic> var. <italic>polyphylla</italic> CS Cheng. Class I <italic>TCP</italic> usually promotes cell proliferation, so its increased expression in <italic>EKP</italic> is also consistent with the phenotype (<xref ref-type="bibr" rid="B33">Li, 2015</xref>). So, these results first suggested that different TCP transcription factors have antagonistic effects on compound leaf development.</p>
<p>In this study, the <italic>EkTCP</italic> genes and other hub genes mentioned in <xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7D</bold>
</xref> were then validated by qRT-PCR analysis. The results showed that the gene expression of <italic>EkTCP14, EkTCP9, EkSERK1 and EkACC2</italic> was consistent with that in RNA-Seq analysis (t-test: N=3, **P &lt; 0.01; *P &lt; 0.05), but the expression of other 4 genes showed no significant difference compared to the discovered newly variety and the normal <italic>E. koreanum</italic>. We also investigated the sequence differences of <italic>EkTCP</italic> between the variety and normal <italic>E.koreanum</italic>, as well as the probable changes in spatial structure and evolutionary relationships. The results showed that <italic>EkTCP9</italic> and <italic>EkTCP14</italic> had multiple SNP sites, however, SNP sites were showed not in the <italic>EkTCP</italic> domain, and only the spatial structure of <italic>EkTCP9</italic> was slightly changed, so we speculated that there was no significant difference in the function of <italic>EkTCP9</italic> and <italic>EkTCP14</italic> (<xref ref-type="supplementary-material" rid="SF2">
<bold>Figures S2A, B</bold>
</xref>). In addition, we also carried out evolutionary analysis on the <italic>EkTCP</italic> of berberaceae, and found that the variation of <italic>EkTCP</italic> did not change much in evolution, were closest relatives to <italic>Papaver somniferum</italic> and <italic>Coptis chinensis</italic> (<xref ref-type="supplementary-material" rid="SF2">
<bold>Figure S2C</bold>
</xref>). Overall, the findings in this work implied that <italic>EkTCP</italic> transcription factors may play an essential role in controlling <italic>E. koreanum</italic> leaf development.</p>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<sec id="s4_1">
<label>4.1</label>
<title>Discovery and identification of new variety of <italic>Epimedium koreanum</italic>
</title>
<p>
<italic>E. koreanum</italic> is a commonly used Chinese herb, and the <italic>Ch. P</italic> records five species of <italic>Epimedium</italic>, which include <italic>E. koreanum</italic>, <italic>E. wushanense</italic>, <italic>E. sagittatum</italic>, <italic>E. pubescens</italic>, and <italic>E. brevicornu</italic>. Our research team has been committed to comprehensively collecting wild <italic>Epimedium</italic> resources on a large scale and across latitudes. During our investigations in the growing area of <italic>E. koreanum</italic> in Dunhua, Jilin Province, we discovered a striking variety of <italic>Epimedium</italic> exhibiting more than 9 and up to 27 leaflets. Through meticulous DNA barcoding analysis, this variety was conclusively identified as a distinctive variety of <italic>E. koreanum</italic> with a remarkable leaf yield. The distribution of this variety within its growing area appears to occur in concentrated patches. Notably, the <italic>Ch. P</italic> has recognized the aboveground parts of <italic>E. koreanum</italic> as a clinical use of Chinese medicine, with leaves gradually replacing other therapeutic portions since 2010 (<xref ref-type="bibr" rid="B46">Qian et&#xa0;al., 2023</xref>). The increased number of leaflets in this newly discovered variety significantly enhances its application value. Furthermore, and the utilization of this resource on breeding and cultivation may contribute to alleviating the existing shortage of <italic>E. koreanumin</italic> the herb market. It is conceivable that the yield of this variety will be much higher than that of other Epimedium species. So, we used comparative RNA-Seq analysis to investigate the process of leaf development after discovering the novel <italic>E. koreanum</italic> varieties.</p>
<p>Currently, the descovered newly variety of <italic>E. koreanum</italic> has been cultivated in the Lushan Botanical Garden for one year, completing a phenological observation of the reproductive cycle. Although the newly identified germplasm still has an advantage in terms of the number of leaflets, the number of leaflets in ex situ grown plants has reduced in comparison to the original plants. The instability in the number of small leaf blades was observed, pointing to an innovative field of investigation into the molecular mechanism of complex leaf development.</p>
</sec>
<sec id="s4_2">
<label>4.2</label>
<title>Identification of hub genes regulating leaf biomass in <italic>E. koreanum</italic> var. <italic>polyphylla</italic> CS Cheng</title>
<p>The regulation of leaf development has been extensively studied in various plant species, including <italic>Arabidopsis</italic> (<xref ref-type="bibr" rid="B27">Koyama et&#xa0;al., 2017</xref>), tomato (<xref ref-type="bibr" rid="B44">Ori et&#xa0;al., 2007</xref>), andmedicago (<xref ref-type="bibr" rid="B14">He et&#xa0;al., 2020</xref>). However, the complete genome sequence of <italic>E. koreanum</italic> is not yet available, making the functional study of its genes particularly challenging. <italic>Epimedium</italic> species, including <italic>E. koreanum</italic>, possess relatively large genomes and undergo numerous interspecific hybridizations, further complicating gene function analysis. To overcome these challenges, we employed RNA-seq, a powerful technique that allows for the analysis of gene expression and phenotypic characteristics. In this study, we performed comparative RNA-seq analysis on different varieties of <italic>E. koreanum</italic> and a control sample of normal <italic>E. koreanum</italic>. Our analysis identified 387 up-regulated genes and 784 down-regulated genes (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). Actually, we intended to uncover essential genes with significant alterations in the hot reported genes associated with plant compound leaf production, and then confirm their function using RT-PCR with a larger sample size (<xref ref-type="supplementary-material" rid="SM1">
<bold>Table S2</bold>
</xref>), However, we found that none of the 10 hot genes mentioned in the study had significant differences between the newly resources and the typical <italic>E. koreanum</italic>. To gain insights into the functional implications of these differentially expressed genes, we conducted Gene Ontology (GO) enrichment analysis, which revealed the top ten most enriched gene categories (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>). These findings significantly contributed to our understanding of <italic>E. koreanum</italic>&#x2019;s flavonoid metabolism and leaf growth processes.</p>
<p>Furthermore, we employed weighted gene co-expression network analysis (WGCNA) to uncover the modular structure and regulatory relationships among the identified genes. By performing network analysis, we successfully identified several hub genes that play a pivotal role in the regulation of leaf development in <italic>Epimedium</italic> (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7A</bold>
</xref>). Notably, our investigation highlighted the relevance of <italic>TCP</italic> family genes in leaf development, a finding supported by studies in other plant species. <italic>TCP</italic> genes have been demonstrated to affect various aspects of leaf development, such as leaf shape (<xref ref-type="bibr" rid="B45">Palatnik et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B47">Qin et&#xa0;al., 2005</xref>; <xref ref-type="bibr" rid="B51">Schommer et&#xa0;al., 2008</xref>), size (<xref ref-type="bibr" rid="B10">Efroni et&#xa0;al., 2008</xref>; <xref ref-type="bibr" rid="B55">Tao et&#xa0;al., 2013</xref>), senescence (<xref ref-type="bibr" rid="B7">Danisman et&#xa0;al., 2013</xref>) and complexity (<xref ref-type="bibr" rid="B26">Koyama et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B49">Rubio-Somoza et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B58">Viola et&#xa0;al., 2023</xref>). Based on the integration of RNA-seq data and bioinformatics analysis, we made a significant discovery by identifying hub genes that are crucial for the regulation of leaf growth and development in <italic>Epimedium</italic>. These findings enhance our understanding of the molecular mechanisms underlying leaf growth and hold promise for potential applications in <italic>Epimedium</italic> breeding and leaf biomass improvement.</p>
<p>Currently, Transcriptome sequencing is the most effective approach for identifying differentially expressed genes in wild samples. It is required to investigate the spatiotemporal expression of genes involved to compound leaf development using real-time fluorescence quantification under an environmental control conditions. Specifically, absolute quantification of gene expression levels in samples with a gradient in leaflet number can assist discover the critical genes and regulatory mechanisms determining compound leaf biomass. In our validation study of differential gene expressions by using qRT-PCR analysis under an equal environmental control conditions, the results showed that the gene expression of EkTCP14, EkTCP9, EkSERK1 and EkACC2 was obvious consistent with that in RNA-Seq analysis, but the other 4 gene expressions showed no significant difference compared to the discovered newly variety and the normal <italic>E. koreanum.</italic> We speculate that the reason for this predicament is that direct transcriptome sequencing utilizing wild plant samples might provide some false positive findings. Therefore, the results of the qRT-PCR investigation revealed the regulatory involvement of the <italic>EkTCP</italic> transcription factors in the development of compound leaves.</p>
</sec>
<sec id="s4_3">
<label>4.3</label>
<title>Phytohormone regulates leaf development</title>
<p>Leaf development in plants is regulated by various phytohormones, including auxin and cytokinin (<xref ref-type="bibr" rid="B43">Navarro-Cartagena and Micol, 2023</xref>). The morphology of leaves varies across different plant species, primarily due to the distinct arrangement of leaf lobes or teeth in single leaves and leaflets in compound leaves (<xref ref-type="bibr" rid="B13">Hay and Tsiantis, 2006</xref>; <xref ref-type="bibr" rid="B50">Runions et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B22">Kierzkowski et&#xa0;al., 2019</xref>). Cytokinin plays a significant role in regulating leaf complexity in compound leaf species such as tomato and cardamine (<italic>Cardamine hirsuta</italic>). Additionally, in simple leaf species like <italic>Arabidopsis thaliana</italic>, both cytokinin and auxin co-regulate the morphogenesis of leaf margins. Transcription factors belonging to the <italic>TCP</italic> family are essential for maintaining the balance between cell proliferation and differentiation during leaf development. Class I <italic>TCP</italic> family members promote cell proliferation, while class II family members repress cell proliferation (<xref ref-type="bibr" rid="B33">Li, 2015</xref>). In <italic>Arabidopsis</italic>, Class I TCPs have been found to promote cytokinin responses (<xref ref-type="bibr" rid="B52">Steiner et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B53">Steiner et&#xa0;al., 2016</xref>).Notably, the up-regulation of Class II <italic>TCPs</italic> and <italic>KNOX2</italic> genes has been shown to repress the expression levels of <italic>KNOX1</italic> and <italic>CUP-SHAPED COTYLEDON</italic>(<italic>CUC2</italic>), thereby enhancing cytokinin response in Nicotiana tabacum <italic>BY-2</italic> protoplasts and increasing the levels of active cytokinin (<xref ref-type="bibr" rid="B6">Cucinotta et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B5">Cucinotta et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B3">Challa et&#xa0;al., 2021</xref>).</p>
<p>Our findings indicate that the expression of <italic>TCPs</italic> in <italic>EKP</italic> significantly differed from that of normal <italic>E. koreanum</italic>. This suggested that abnormal leaf development in <italic>EKP</italic> might be regulated through phytohormone mediated abnormal expression of <italic>TCPs</italic>. However, it is important to note that we were unable to identify any genes directly involved in cytokinin regulation in this study. Although these genes may potentially exist, their specific functions remain unknown due to the lack of comprehensive genomic information. In conclusion, our study highlights the crucial roles of auxin and cytokinin in regulating leaf development. The complex interplay between phytohormones and key transcription factors, such as <italic>TCPs</italic>, is fundamental for determining leaf morphology and complexity across plant species. Further research is needed to unravel the precise mechanisms underlying cytokine in regulation and its direct genetic targets, which will contribute to a comprehensive understanding of leaf development in plants.</p>
</sec>
</sec>
<sec id="s5" sec-type="conclusions">
<label>5</label>
<title>Conclusion</title>
<p>In this study, we have discovered a new class of <italic>Epimedium</italic> resources. Through DNA barcoding and phylogenetic tree analysis, it is believed that it belongs to the <italic>E. koreanum</italic> variety. This discovery not only identified a high leaf biomass of <italic>Epimedium</italic> and expanded the number of varieties of <italic>Epimedium</italic>, but also alleviated the current situation of resource shortage of <italic>Epimedium</italic>. Then, we analyzed the hub genes regulating the leaf biomass of <italic>E. koreanum</italic> through RNA-seq data. Based on the literature reports of related homologous genes and validation of differential gene expressions by qRT-PCR analysis, we suggested that <italic>EkTCP9</italic> and <italic>EkTCP14</italic> transcription factors play an important role in the leaf development of <italic>E. koreanum</italic>. The level of their expression was in line with expectations. We also investigated the SNP sites and possible spatial structure of these two <italic>EkTCP</italic>, and found that the <italic>EkTCP</italic> of these two <italic>E. koreanum</italic> has multiple SNP sites, but there was no significant effect on their spatial structure. In conclusion, our study not only found a new variety of <italic>E. koreanum</italic>, but also preliminarily analyzed the hub genes that regulate leaf development, providing new insights for future breeding of <italic>Epimedium</italic> with high leaf biomass.</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: Bioproject accession number PRJNA1008345.</p>
</sec>
<sec id="s7" sec-type="author-contributions">
<title>Author contributions</title>
<p>JY: Investigation, Writing &#x2013; original draft, Formal analysis, Methodology, Software. SF: Investigation, Methodology, Software, Data curation. ZX &amp; MG: Methodology, Validation. QC: Methodology, Validation, Investigation, Software. PG: Writing &#x2013; review &amp; editing. CC: Investigation, Writing &#x2013; review &amp; editing, Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Writing &#x2013; original draft.</p>
</sec>
</body>
<back>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by grants from National Natural Science Foundation of China (No.82260746). The authors gratefully acknowledge financial supports from Jiangxi Province Double Thousand Talent-Leader of Natural Science Project (jxsq2023101038), Jiangxi Province Urgently Overseas Talent Project (2022BCJ25027 &amp; 2023BBG70014), Lushan Botanical Garden Project (2022ZWZX07 &amp; 2023ZWZX08) and the Science and Technology Innovation Team Project in Key Areas of Jiujiang City Base and Talent Plan (S2022TDJS029).</p>
</sec>
<sec id="s9" 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="s10" 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>
<sec id="s11" 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.2023.1290836/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fpls.2023.1290836/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="Image_1.jpeg" id="SF1" mimetype="image/jpeg">
<label>Supplementary Figure&#xa0;1</label>
<caption>
<p>Distribution of <italic>E. perralderianum, E. pinnatum</italic>and <italic>E. koreanum.</italic> The distribution of three species of <italic>Epimedium</italic> on the map. The red triangles represent different sample aera.</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Image_2.jpeg" id="SF2" mimetype="image/jpeg">
<label>Supplementary Figure&#xa0;2</label>
<caption>
<p>Evolutionary relationships of TCP-containing proteins of <italic>E. koreanum.</italic> <bold>(A)</bold> SNP sites of <italic>EkTCP9</italic> and <italic>EkTCP14. EkTCP14-1</italic> and <italic>EkTCP9-1</italic> extracted from <italic>E. kroeanum</italic>, <italic>EkTCP14-2</italic> and <italic>EkTCP9-2</italic> extracted from <italic>E. koreanum</italic>var.<italic>polyphylla</italic> CS Cheng. <bold>(B)</bold>The spatial structure of TCP9 and TCP14.The red arrows represent the distinct areas. <bold>(C)</bold> The optimal tree with the sum of branch length = 14.79 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances are in the units of the number of amino acid substitutions per site. The analysis involved 298 amino acid sequences with <italic>TCP</italic> domains, of which 294 were from the order Ranunculales. All positions containing gaps and missing data were eliminated.</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Table_1.docx" id="SF3" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document">
<label>Supplementary Table&#xa0;1</label>
<caption>
<p>Differentially expressed transcripts in variety Compared with normal <italic>E. koreanum.</italic>
</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Table_2.docx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document"/>
</sec>
<ref-list>
<title>References</title>
<ref id="B1">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Bar</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Ori</surname> <given-names>N.</given-names>
</name>
</person-group> (<year>2015</year>). <article-title>Compound leaf development in model plant species</article-title>. <source>Curr. Opin. Plant Biol.</source> <volume>23</volume>, <fpage>61</fpage>&#x2013;<lpage>69</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.pbi.2014.10.007</pub-id>
</citation>
</ref>
<ref id="B2">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Castresana</surname> <given-names>J.</given-names>
</name>
</person-group> (<year>2000</year>). <article-title>Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis</article-title>. <source>Mol. Biol. Evol.</source> <volume>17</volume>, <fpage>540</fpage>&#x2013;<lpage>552</lpage>. doi: <pub-id pub-id-type="doi">10.1093/oxfordjournals.molbev.a026334</pub-id>
</citation>
</ref>
<ref id="B3">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Challa</surname> <given-names>K. R.</given-names>
</name>
<name>
<surname>Rath</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Sharma</surname> <given-names>A. N.</given-names>
</name>
<name>
<surname>Bajpai</surname> <given-names>A. K.</given-names>
</name>
<name>
<surname>Davuluri</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Acharya</surname> <given-names>K. K.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>Active suppression of leaflet emergence as a mechanism of simple leaf development</article-title>. <source>Nat. Plants</source> <volume>7</volume>, <fpage>1264</fpage>&#x2013;<lpage>1275</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/s41477-021-00965-3</pub-id>
</citation>
</ref>
<ref id="B4">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Chen</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Zhou</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Gu</surname> <given-names>J.</given-names>
</name>
</person-group> (<year>2018</year>). <article-title>fastp: an ultra-fast all-in-one FASTQ preprocessor</article-title>. <source>Bioinf. (Oxford England)</source> <volume>34</volume>, <fpage>i884</fpage>&#x2013;<lpage>i890</lpage>. doi: <pub-id pub-id-type="doi">10.1093/bioinformatics/bty560</pub-id>
</citation>
</ref>
<ref id="B5">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Cucinotta</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Di Marzo</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Guazzotti</surname> <given-names>A.</given-names>
</name>
<name>
<surname>de Folter</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Kater</surname> <given-names>M. M.</given-names>
</name>
<name>
<surname>Colombo</surname> <given-names>L.</given-names>
</name>
</person-group> (<year>2020</year>). <article-title>Gynoecium size and ovule number are interconnected traits that impact seed yield</article-title>. <source>J. Exp. Bot.</source> <volume>71</volume>, <fpage>2479</fpage>&#x2013;<lpage>2489</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/jxb/eraa050</pub-id>
</citation>
</ref>
<ref id="B6">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Cucinotta</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Manrique</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Cuesta</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Benkova</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Novak</surname> <given-names>O.</given-names>
</name>
<name>
<surname>Colombo</surname> <given-names>L.</given-names>
</name>
</person-group> (<year>2018</year>). <article-title>CUP-SHAPED COTYLEDON1 (CUC1) and CUC2 regulate cytokinin homeostasis to determine ovule number in Arabidopsis</article-title>. <source>J. Exp. Bot.</source> <volume>69</volume>, <fpage>5169</fpage>&#x2013;<lpage>5176</lpage>. doi: <pub-id pub-id-type="doi">10.1093/jxb/ery281</pub-id>
</citation>
</ref>
<ref id="B7">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Danisman</surname> <given-names>S.</given-names>
</name>
<name>
<surname>van Dijk</surname> <given-names>A. D.</given-names>
</name>
<name>
<surname>Bimbo</surname> <given-names>A.</given-names>
</name>
<name>
<surname>van der Wal</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Hennig</surname> <given-names>L.</given-names>
</name>
<name>
<surname>de Folter</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2013</year>). <article-title>Analysis of functional redundancies within the Arabidopsis TCP transcription factor family</article-title>. <source>J. Exp. Bot.</source> <volume>64</volume>, <fpage>5673</fpage>&#x2013;<lpage>5685</lpage>. doi: <pub-id pub-id-type="doi">10.1093/jxb/ert337</pub-id>
</citation>
</ref>
<ref id="B8">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Demason</surname> <given-names>D. A.</given-names>
</name>
<name>
<surname>Chetty</surname> <given-names>V.</given-names>
</name>
<name>
<surname>Barkawi</surname> <given-names>L. S.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Cohen</surname> <given-names>J. D.</given-names>
</name>
</person-group> (<year>2013</year>). <article-title>Unifoliata-Afila interactions in pea leaf morphogenesis</article-title>. <source>Am. J. Bot.</source> <volume>100</volume>, <fpage>478</fpage>&#x2013;<lpage>495</lpage>. doi: <pub-id pub-id-type="doi">10.3732/ajb.1200611</pub-id>
</citation>
</ref>
<ref id="B9">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Dengler</surname> <given-names>N. G.</given-names>
</name>
<name>
<surname>Tsukaya</surname> <given-names>H.</given-names>
</name>
</person-group> (<year>2001</year>). <article-title>Leaf morphogenesis in dicotyledons: current issues</article-title>. <source>Int. J. Plant Sci.</source> <volume>162</volume>, <fpage>459</fpage>&#x2013;<lpage>464</lpage>. doi: <pub-id pub-id-type="doi">10.1086/320145</pub-id>
</citation>
</ref>
<ref id="B10">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Efroni</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Blum</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Goldshmidt</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Eshed</surname> <given-names>Y.</given-names>
</name>
</person-group> (<year>2008</year>). <article-title>A protracted and dynamic maturation schedule underlies Arabidopsis leaf development</article-title>. <source>Plant Cell</source> <volume>20</volume>, <fpage>2293</fpage>&#x2013;<lpage>2306</lpage>. doi: <pub-id pub-id-type="doi">10.1105/tpc.107.057521</pub-id>
</citation>
</ref>
<ref id="B11">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Grabherr</surname> <given-names>M. G.</given-names>
</name>
<name>
<surname>Haas</surname> <given-names>B. J.</given-names>
</name>
<name>
<surname>Yassour</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Levin</surname> <given-names>J. Z.</given-names>
</name>
<name>
<surname>Thompson</surname> <given-names>D. A.</given-names>
</name>
<name>
<surname>Amit</surname> <given-names>I.</given-names>
</name>
<etal/>
</person-group>. (<year>2011</year>). <article-title>Full-length transcriptome assembly from RNA-Seq data without a reference genome</article-title>. <source>Nat. Biotechnol.</source> <volume>29</volume>, <fpage>644</fpage>&#x2013;<lpage>652</lpage>. doi: <pub-id pub-id-type="doi">10.1038/nbt.1883</pub-id>
</citation>
</ref>
<ref id="B12">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Guo</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Pang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Jiang</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Liao</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Yu</surname> <given-names>J.</given-names>
</name>
<etal/>
</person-group>. (<year>2022</year>). <article-title>Plastid genome data provide new insights into the phylogeny and evolution of the genus Epimedium</article-title>. <source>J. Adv. Res.</source> <volume>36</volume>, <fpage>175</fpage>&#x2013;<lpage>185</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.jare.2021.06.020</pub-id>
</citation>
</ref>
<ref id="B13">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Hay</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Tsiantis</surname> <given-names>M.</given-names>
</name>
</person-group> (<year>2006</year>). <article-title>The genetic basis for differences in leaf form between Arabidopsis thaliana and its wild relative Cardamine hirsuta</article-title>. <source>Nat. Genet.</source> <volume>38</volume>, <fpage>942</fpage>&#x2013;<lpage>947</lpage>. doi: <pub-id pub-id-type="doi">10.1038/ng1835</pub-id>
</citation>
</ref>
<ref id="B14">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>He</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>He</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Qi</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>X.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>A molecular framework underlying the compound leaf pattern of Medicago truncatula</article-title>. <source>Nat. Plants</source> <volume>6</volume>, <fpage>511</fpage>&#x2013;<lpage>521</lpage>. doi: <pub-id pub-id-type="doi">10.1038/s41477-020-0642-2</pub-id>
</citation>
</ref>
<ref id="B15">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Helliwell</surname> <given-names>E. E.</given-names>
</name>
<name>
<surname>Vega-Arregu&#xed;n</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Shi</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Bailey</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Xiao</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Maximova</surname> <given-names>S. N.</given-names>
</name>
<etal/>
</person-group>. (<year>2016</year>). <article-title>Enhanced resistance in Theobroma cacao against oomycete and fungal pathogens by secretion of phosphatidylinositol-3-phosphate-binding proteins</article-title>. <source>Plant Biotechnol. J.</source> <volume>14</volume>, <fpage>875</fpage>&#x2013;<lpage>886</lpage>. doi: <pub-id pub-id-type="doi">10.1111/pbi.12436</pub-id>
</citation>
</ref>
<ref id="B16">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Indran</surname> <given-names>I. R.</given-names>
</name>
<name>
<surname>Liang</surname> <given-names>R. L.</given-names>
</name>
<name>
<surname>Min</surname> <given-names>T. E.</given-names>
</name>
<name>
<surname>Yong</surname> <given-names>E. L.</given-names>
</name>
</person-group> (<year>2016</year>). <article-title>Preclinical studies and clinical evaluation of compounds from the genus Epimedium for osteoporosis and bone health</article-title>. <source>Pharmacol. Ther.</source> <volume>162</volume>, <fpage>188</fpage>&#x2013;<lpage>205</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.pharmthera.2016.01.015</pub-id>
</citation>
</ref>
<ref id="B17">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Jiang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Song</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Jia</surname> <given-names>X. B.</given-names>
</name>
</person-group> (<year>2015</year>). <article-title>Phytochemistry and ethnopharmacology of epimedium L. Species</article-title>. <source>Chin. Herb. Med.</source> <volume>7</volume>, <fpage>204</fpage>&#x2013;<lpage>222</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/S1674-6384(15)60043-0</pub-id>
</citation>
</ref>
<ref id="B18">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Jiao</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Sun</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>An</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Fu</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>W.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>Improvement of Qilin pills on male reproductive function in tripterygium glycoside-induced oligoasthenospermia in rats</article-title>. <source>Andrologia</source> <volume>53</volume>, <elocation-id>e13923</elocation-id>. doi: <pub-id pub-id-type="doi">10.1111/and.13923</pub-id>
</citation>
</ref>
<ref id="B19">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Katoh</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Standley</surname> <given-names>D. M.</given-names>
</name>
</person-group> (<year>2013</year>). <article-title>MAFFT multiple sequence alignment software version 7: improvements in performance and usability</article-title>. <source>Mol. Biol. Evol.</source> <volume>30</volume>, <fpage>772</fpage>&#x2013;<lpage>780</lpage>. doi: <pub-id pub-id-type="doi">10.1093/molbev/mst010</pub-id>
</citation>
</ref>
<ref id="B20">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kearse</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Moir</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Wilson</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Stones-Havas</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Cheung</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Sturrock</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2012</year>). <article-title>Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data</article-title>. <source>Bioinf. (Oxford England)</source> <volume>28</volume>, <fpage>1647</fpage>&#x2013;<lpage>1649</lpage>. doi: <pub-id pub-id-type="doi">10.1093/bioinformatics/bts199</pub-id>
</citation>
</ref>
<ref id="B21">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kieffer</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Master</surname> <given-names>V.</given-names>
</name>
<name>
<surname>Waites</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Davies</surname> <given-names>B.</given-names>
</name>
</person-group> (<year>2011</year>). <article-title>TCP14 and TCP15 affect internode length and leaf shape in Arabidopsis</article-title>. <source>Plant J.</source> <volume>68</volume>, <fpage>147</fpage>&#x2013;<lpage>158</lpage>. doi: <pub-id pub-id-type="doi">10.1111/j.1365-313X.2011.04674.x</pub-id>
</citation>
</ref>
<ref id="B22">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kierzkowski</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Runions</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Vuolo</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Strauss</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Lymbouridou</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Routier-Kierzkowska</surname> <given-names>A. L.</given-names>
</name>
<etal/>
</person-group>. (<year>2019</year>). <article-title>A growth-based framework for leaf shape development and diversity</article-title>. <source>Cell</source> <volume>177</volume>, <fpage>1405</fpage>&#x2013;<lpage>1418.e1417</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.cell.2019.05.011</pub-id>
</citation>
</ref>
<ref id="B23">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kim</surname> <given-names>W. J.</given-names>
</name>
<name>
<surname>Ji</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Choi</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Kang</surname> <given-names>Y. M.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Moon</surname> <given-names>B. C.</given-names>
</name>
</person-group> (<year>2016</year>). <article-title>Molecular identification and phylogenetic analysis of important medicinal plant species in genus Paeonia based on rDNA-ITS, matK, and rbcL DNA barcode sequences. Genet</article-title>. <source>Mol. Res.</source> <volume>15</volume> (<issue>3</issue>), <fpage>gmr.15038472</fpage>. doi: <pub-id pub-id-type="doi">10.4238/gmr.15038472</pub-id>
</citation>
</ref>
<ref id="B24">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kim</surname> <given-names>H. S.</given-names>
</name>
<name>
<surname>Lee</surname> <given-names>B. Y.</given-names>
</name>
<name>
<surname>Won</surname> <given-names>E. J.</given-names>
</name>
<name>
<surname>Han</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Hwang</surname> <given-names>D. S.</given-names>
</name>
<name>
<surname>Park</surname> <given-names>H. G.</given-names>
</name>
<etal/>
</person-group>. (<year>2015</year>). <article-title>Identification of xenobiotic biodegradation and metabolism-related genes in the copepod Tigriopus japonicus whole transcriptome analysis</article-title>. <source>Mar. Genomics</source> <volume>24 Pt 3</volume>, <fpage>207</fpage>&#x2013;<lpage>208</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.margen.2015.05.011</pub-id>
</citation>
</ref>
<ref id="B25">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kim</surname> <given-names>M.</given-names>
</name>
<name>
<surname>McCormick</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Timmermans</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Sinha</surname> <given-names>N.</given-names>
</name>
</person-group> (<year>2003</year>). <article-title>The expression domain of PHANTASTICA determines leaflet placement in compound leaves</article-title>. <source>Nature</source> <volume>424</volume>, <fpage>438</fpage>&#x2013;<lpage>443</lpage>. doi: <pub-id pub-id-type="doi">10.1038/nature01820</pub-id>
</citation>
</ref>
<ref id="B26">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Koyama</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Mitsuda</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Seki</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Shinozaki</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Ohme-Takagi</surname> <given-names>M.</given-names>
</name>
</person-group> (<year>2010</year>). <article-title>TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis</article-title>. <source>Plant Cell</source> <volume>22</volume>, <fpage>3574</fpage>&#x2013;<lpage>3588</lpage>. doi: <pub-id pub-id-type="doi">10.1105/tpc.110.075598</pub-id>
</citation>
</ref>
<ref id="B27">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Koyama</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Sato</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Ohme-Takagi</surname> <given-names>M.</given-names>
</name>
</person-group> (<year>2017</year>). <article-title>Roles of miR319 and TCP transcription factors in leaf development</article-title>. <source>Plant Physiol.</source> <volume>175</volume>, <fpage>874</fpage>&#x2013;<lpage>885</lpage>. doi: <pub-id pub-id-type="doi">10.1104/pp.17.00732</pub-id>
</citation>
</ref>
<ref id="B28">
<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>Mol. Biol. Evol.</source> <volume>35</volume>, <fpage>1547</fpage>&#x2013;<lpage>1549</lpage>. doi: <pub-id pub-id-type="doi">10.1093/molbev/msy096</pub-id>
</citation>
</ref>
<ref id="B29">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Langfelder</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Horvath</surname> <given-names>S.</given-names>
</name>
</person-group> (<year>2008</year>). <article-title>WGCNA: an R package for weighted correlation network analysis</article-title>. <source>BMC Bioinform.</source> <volume>9</volume>, <fpage>559</fpage>. doi: <pub-id pub-id-type="doi">10.1186/1471-2105-9-559</pub-id>
</citation>
</ref>
<ref id="B30">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Langmead</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Salzberg</surname> <given-names>S. L.</given-names>
</name>
</person-group> (<year>2012</year>). <article-title>Fast gapped-read alignment with Bowtie 2</article-title>. <source>Nat. Methods</source> <volume>9</volume>, <fpage>357</fpage>&#x2013;<lpage>359</lpage>. doi: <pub-id pub-id-type="doi">10.1038/nmeth.1923</pub-id>
</citation>
</ref>
<ref id="B31">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Laura</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Angela</surname> <given-names>T. M.</given-names>
</name>
<name>
<surname>Will</surname> <given-names>E.</given-names>
</name>
</person-group> (<year>2010</year>). <article-title>Not so simple after all: searching for ecological advantages of compound leaves</article-title>. <source>Oikos</source> <volume>120</volume>, <fpage>813</fpage>&#x2013;<lpage>821</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/j.1600-0706.2010.19344.x</pub-id>
</citation>
</ref>
<ref id="B32">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Lee</surname> <given-names>J. H.</given-names>
</name>
<name>
<surname>Kim</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Kim</surname> <given-names>N. R.</given-names>
</name>
<name>
<surname>Lee</surname> <given-names>S. C.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>T. J.</given-names>
</name>
<name>
<surname>Kim</surname> <given-names>Y. D.</given-names>
</name>
</person-group> (<year>2016</year>). <article-title>The complete chloroplast genome of a medicinal plant Epimedium koreanum Nakai (Berberidaceae)</article-title>. <source>Mitochondrial. DNA A DNA Mapp Seq Anal.</source> <volume>27</volume>, <fpage>4342</fpage>&#x2013;<lpage>4343</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.3109/19401736.2015.1089492</pub-id>
</citation>
</ref>
<ref id="B33">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Li</surname> <given-names>S.</given-names>
</name>
</person-group> (<year>2015</year>). <article-title>The Arabidopsis thaliana TCP transcription factors: A broadening horizon beyond development</article-title>. <source>Plant Signal. Behav.</source> <volume>10</volume>, <elocation-id>e1044192</elocation-id>. doi: <pub-id pub-id-type="doi">10.1080/15592324.2015.1044192</pub-id>
</citation>
</ref>
<ref id="B34">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Li</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Dewey</surname> <given-names>C. N.</given-names>
</name>
</person-group> (<year>2011</year>). <article-title>RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome</article-title>. <source>BMC Bioinform.</source> <volume>12</volume>, <fpage>323</fpage>. doi: <pub-id pub-id-type="doi">10.1186/1471-2105-12-323</pub-id>
</citation>
</ref>
<ref id="B35">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Li</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Gao</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Zhu</surname> <given-names>Z.</given-names>
</name>
<etal/>
</person-group>. (<year>2009</year>). <article-title>Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster</article-title>. <source>Nucleic Acids Res.</source> <volume>37</volume>, <fpage>4308</fpage>&#x2013;<lpage>4314</lpage>. doi: <pub-id pub-id-type="doi">10.1093/nar/gkp334</pub-id>
</citation>
</ref>
<ref id="B36">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Li</surname> <given-names>S. Q.</given-names>
</name>
<name>
<surname>Pei</surname> <given-names>Z. G.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Y. M.</given-names>
</name>
</person-group> (<year>2001</year>). <article-title>Clinical study on effect of gushukang granule in preventing and treating primary osteoporosis</article-title>. <source>Zhongguo Zhong xi yi jie he za zhi Zhongguo Zhongxiyi jiehe zazhi = Chin. J. integrated traditional Western Med.</source> <volume>21</volume>, <fpage>265</fpage>&#x2013;<lpage>268</lpage>.</citation>
</ref>
<ref id="B37">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Lin</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Jin</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Zong</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Yu</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Zhu</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>G.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>High-efficiency prime editing with optimized, paired pegRNAs in plants</article-title>. <source>Nat. Biotechnol.</source> <volume>39</volume>, <fpage>923</fpage>&#x2013;<lpage>927</lpage>. doi: <pub-id pub-id-type="doi">10.1038/s41587-021-00868-w</pub-id>
</citation>
</ref>
<ref id="B38">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liu</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Qiu</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>C.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>Pharmacokinetic-pharmacodynamic modeling analysis and anti-inflammatory effect of Wangbi capsule in the treatment of adjuvant-induced arthritis</article-title>. <source>Biomed. Chromatogr.</source> <volume>35</volume>, <elocation-id>e5101</elocation-id>. doi: <pub-id pub-id-type="doi">10.1002/bmc.5101</pub-id>
</citation>
</ref>
<ref id="B39">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Love</surname> <given-names>M. I.</given-names>
</name>
<name>
<surname>Huber</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Anders</surname> <given-names>S.</given-names>
</name>
</person-group> (<year>2014</year>). <article-title>Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2</article-title>. <source>Genome Biol.</source> <volume>15</volume>, <fpage>550</fpage>. doi: <pub-id pub-id-type="doi">10.1186/s13059-014-0550-8</pub-id>
</citation>
</ref>
<ref id="B40">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Luo</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Ning</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>J.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2 in lettuce</article-title>. <source>Hortic. Res.</source> <volume>8</volume>, <fpage>184</fpage>. doi: <pub-id pub-id-type="doi">10.1038/s41438-021-00622-y</pub-id>
</citation>
</ref>
<ref id="B41">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ma</surname> <given-names>H.</given-names>
</name>
<name>
<surname>He</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Hao</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Jia</surname> <given-names>Z.</given-names>
</name>
</person-group> (<year>2011</year>). <article-title>The genus Epimedium: an ethnopharmacological and phytochemical review</article-title>. <source>J. Ethnopharmacol.</source> <volume>134</volume>, <fpage>519</fpage>&#x2013;<lpage>541</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.jep.2011.01.001</pub-id>
</citation>
</ref>
<ref id="B42">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Mishra</surname> <given-names>R. K.</given-names>
</name>
<name>
<surname>Chaudhary</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Kumar</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Kumar</surname> <given-names>S.</given-names>
</name>
</person-group> (<year>2009</year>). <article-title>Effects of MULTIFOLIATE-PINNA, AFILA, TENDRIL-LESS and UNIFOLIATA genes on leafblade architecture in Pisum sativum</article-title>. <source>Planta</source> <volume>230</volume>, <fpage>177</fpage>&#x2013;<lpage>190</lpage>. doi: <pub-id pub-id-type="doi">10.1007/s00425-009-0931-5</pub-id>
</citation>
</ref>
<ref id="B43">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Navarro-Cartagena</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Micol</surname> <given-names>J. L.</given-names>
</name>
</person-group> (<year>2023</year>). <article-title>Is auxin enough? Cytokinins and margin patterning in simple leaves</article-title>. <source>Trends Plant Sci.</source> <volume>28</volume>, <fpage>54</fpage>&#x2013;<lpage>73</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.tplants.2022.08.019</pub-id>
</citation>
</ref>
<ref id="B44">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ori</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Cohen</surname> <given-names>A. R.</given-names>
</name>
<name>
<surname>Etzioni</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Brand</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Yanai</surname> <given-names>O.</given-names>
</name>
<name>
<surname>Shleizer</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2007</year>). <article-title>Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato</article-title>. <source>Nat. Genet.</source> <volume>39</volume>, <fpage>787</fpage>&#x2013;<lpage>791</lpage>. doi: <pub-id pub-id-type="doi">10.1038/ng2036</pub-id>
</citation>
</ref>
<ref id="B45">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Palatnik</surname> <given-names>J. F.</given-names>
</name>
<name>
<surname>Allen</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Schommer</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Schwab</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Carrington</surname> <given-names>J. C.</given-names>
</name>
<etal/>
</person-group>. (<year>2003</year>). <article-title>Control of leaf morphogenesis by microRNAs</article-title>. <source>Nature</source> <volume>425</volume>, <fpage>257</fpage>&#x2013;<lpage>263</lpage>. doi: <pub-id pub-id-type="doi">10.1038/nature01958</pub-id>
</citation>
</ref>
<ref id="B46">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Qian</surname> <given-names>H. Q.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>D. C.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>C. Y.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>X. R.</given-names>
</name>
<name>
<surname>Han</surname> <given-names>X. K.</given-names>
</name>
<name>
<surname>Peng</surname> <given-names>Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2023</year>). <article-title>A systematic review of traditional uses, phytochemistry, pharmacology and toxicity of Epimedium koreanum Nakai</article-title>. <source>J. Ethnopharmacol.</source> <volume>318</volume>, <fpage>116957</fpage>. doi: <pub-id pub-id-type="doi">10.1016/j.jep.2023.116957</pub-id>
</citation>
</ref>
<ref id="B47">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Qin</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Gu</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Shi</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2005</year>). <article-title>An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development</article-title>. <source>Plant Cell</source> <volume>17</volume>, <fpage>2693</fpage>&#x2013;<lpage>2704</lpage>. doi: <pub-id pub-id-type="doi">10.1105/tpc.105.034959</pub-id>
</citation>
</ref>
<ref id="B48">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ren</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>M.-y.</given-names>
</name>
<name>
<surname>Pang</surname> <given-names>X.-h.</given-names>
</name>
</person-group> (<year>2018</year>). <article-title>Identification and classification of medicinal plants in Epimedium</article-title>. <source>Chin. Herb. Med.</source> <volume>10</volume>, <fpage>249</fpage>&#x2013;<lpage>254</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.chmed.2018.05.004</pub-id>
</citation>
</ref>
<ref id="B49">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Rubio-Somoza</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Zhou</surname> <given-names>C. M.</given-names>
</name>
<name>
<surname>Confraria</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Martinho</surname> <given-names>C.</given-names>
</name>
<name>
<surname>von Born</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Baena-Gonzalez</surname> <given-names>E.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>Temporal control of leaf complexity by miRNA-regulated licensing of protein complexes</article-title>. <source>Curr. Biol.</source> <volume>24</volume>, <fpage>2714</fpage>&#x2013;<lpage>2719</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.cub.2014.09.058</pub-id>
</citation>
</ref>
<ref id="B50">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Runions</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Tsiantis</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Prusinkiewicz</surname> <given-names>P.</given-names>
</name>
</person-group> (<year>2017</year>). <article-title>A common developmental program can produce diverse leaf shapes</article-title>. <source>New Phytol.</source> <volume>216</volume>, <fpage>401</fpage>&#x2013;<lpage>418</lpage>. doi: <pub-id pub-id-type="doi">10.1111/nph.14449</pub-id>
</citation>
</ref>
<ref id="B51">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Schommer</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Palatnik</surname> <given-names>J. F.</given-names>
</name>
<name>
<surname>Aggarwal</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Ch&#xe9;telat</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Cubas</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Farmer</surname> <given-names>E. E.</given-names>
</name>
<etal/>
</person-group>. (<year>2008</year>). <article-title>Control of jasmonate biosynthesis and senescence by miR319 targets</article-title>. <source>PloS Biol.</source> <volume>6</volume>, <elocation-id>e230</elocation-id>. doi: <pub-id pub-id-type="doi">10.1371/journal.pbio.0060230</pub-id>
</citation>
</ref>
<ref id="B52">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Steiner</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Efroni</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Gopalraj</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Saathoff</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Tseng</surname> <given-names>T. S.</given-names>
</name>
<name>
<surname>Kieffer</surname> <given-names>M.</given-names>
</name>
<etal/>
</person-group>. (<year>2012</year>). <article-title>The Arabidopsis O-linked N-acetylglucosamine transferase SPINDLY interacts with class I TCPs to facilitate cytokinin responses in leaves and flowers</article-title>. <source>Plant Cell</source> <volume>24</volume>, <fpage>96</fpage>&#x2013;<lpage>108</lpage>. doi: <pub-id pub-id-type="doi">10.1105/tpc.111.093518</pub-id>
</citation>
</ref>
<ref id="B53">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Steiner</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Livne</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Kobinson-Katz</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Tal</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Pri-Tal</surname> <given-names>O.</given-names>
</name>
<name>
<surname>Mosquna</surname> <given-names>A.</given-names>
</name>
<etal/>
</person-group>. (<year>2016</year>). <article-title>The putative O-linked N-acetylglucosamine transferase SPINDLY inhibits class I TCP proteolysis to promote sensitivity to cytokinin</article-title>. <source>Plant Physiol.</source> <volume>171</volume>, <fpage>1485</fpage>&#x2013;<lpage>1494</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1104/pp.16.00343</pub-id>
</citation>
</ref>
<ref id="B54">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Tamura</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Stecher</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Peterson</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Filipski</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Kumar</surname> <given-names>S.</given-names>
</name>
</person-group> (<year>2013</year>). <article-title>MEGA6: molecular evolutionary genetics analysis version 6.0</article-title>. <source>Mol. Biol. Evol.</source> <volume>30</volume>, <fpage>2725</fpage>&#x2013;<lpage>2729</lpage>. doi: <pub-id pub-id-type="doi">10.1093/molbev/mst197</pub-id>
</citation>
</ref>
<ref id="B55">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Tao</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Wei</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Pang</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Jiang</surname> <given-names>H.</given-names>
</name>
<etal/>
</person-group>. (<year>2013</year>). <article-title>The TIE1 transcriptional repressor links TCP transcription factors with TOPLESS/TOPLESS-RELATED corepressors and modulates leaf development in Arabidopsis</article-title>. <source>Plant Cell</source> <volume>25</volume>, <fpage>421</fpage>&#x2013;<lpage>437</lpage>. doi: <pub-id pub-id-type="doi">10.1105/tpc.113.109223</pub-id>
</citation>
</ref>
<ref id="B56">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Urano</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Maruyama</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Koyama</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Gonzalez</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Inz&#xe9;</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Yamaguchi-Shinozaki</surname> <given-names>K.</given-names>
</name>
<etal/>
</person-group>. (<year>2022</year>). <article-title>CIN-like TCP13 is essential for plant growth regulation under dehydration stress</article-title>. <source>Plant Mol. Biol.</source> <volume>108</volume>, <fpage>257</fpage>&#x2013;<lpage>275</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s11103-021-01238-5</pub-id>
</citation>
</ref>
<ref id="B57">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Vijayan</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Tsou</surname> <given-names>C.H.J.C.S.</given-names>
</name>
</person-group> (<year>2010</year>). <article-title>DNA barcoding in plants: taxonomy in a new perspective</article-title>. <source>Curr. Sci.</source> <volume>99</volume>, <fpage>1530</fpage>&#x2013;<lpage>1541</lpage>. </citation>
</ref>
<ref id="B58">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Viola</surname> <given-names>I. L.</given-names>
</name>
<name>
<surname>Alem</surname> <given-names>A. L.</given-names>
</name>
<name>
<surname>Jure</surname> <given-names>R. M.</given-names>
</name>
<name>
<surname>Gonzalez</surname> <given-names>D. H.</given-names>
</name>
</person-group> (<year>2023</year>). <article-title>Physiological roles and mechanisms of action of class I TCP transcription factors</article-title>. <source>Int. J. Mol. Sci</source> <volume>24</volume> (<issue>6</issue>), <fpage>5437</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.3390/ijms24065437</pub-id>
</citation>
</ref>
<ref id="B59">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Waterhouse</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Bertoni</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Bienert</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Studer</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Tauriello</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Gumienny</surname> <given-names>R.</given-names>
</name>
<etal/>
</person-group>. (<year>2018</year>). <article-title>SWISS-MODEL: homology modelling of protein structures and complexes</article-title>. <source>Nucleic Acids Res.</source> <volume>46</volume>, <fpage>W296</fpage>&#x2013;<lpage>W303</lpage>. doi: <pub-id pub-id-type="doi">10.1093/nar/gky427</pub-id>
</citation>
</ref>
<ref id="B60">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wu</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Dai</surname> <given-names>Z.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>clusterProfiler 4.0: A universal enrichment tool for interpreting omics data</article-title>. <source>Innovation</source> <volume>2</volume>, <fpage>100141</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.xinn.2021.100141</pub-id>
</citation>
</ref>
<ref id="B61">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Du</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>W.</given-names>
</name>
<etal/>
</person-group>. (<year>2016</year>). <article-title>The complete chloroplast genome sequences of five epimedium species: lights into phylogenetic and taxonomic analyses</article-title>. <source>Front. Plant Sci.</source> <volume>7</volume>, <elocation-id>306</elocation-id>. doi: <pub-id pub-id-type="doi">10.3389/fpls.2016.00306</pub-id>
</citation>
</ref>
<ref id="B62">
<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>J.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Liang</surname> <given-names>Q.</given-names>
</name>
</person-group> (<year>2022</year>). <article-title>Taxonomy of Epimedium (Berberidaceae) with special reference to Chinese species</article-title>. <source>Chin. Herb. Med.</source> <volume>14</volume>, <fpage>20</fpage>&#x2013;<lpage>35</lpage>. doi: <pub-id pub-id-type="doi">10.1016/j.chmed.2021.12.001</pub-id>
</citation>
</ref>
<ref id="B63">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>M.-L.</given-names>
</name>
<name>
<surname>Uhink</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Kadereit</surname> <given-names>J.</given-names>
</name>
</person-group> (<year>2007</year>). <article-title>Phylogeny and biogeography of epimedium/vancouveria (Berberidaceae): western north american - east asian disjunctions, the origin of european mountain plant taxa, and east asian species diversity</article-title>. <source>Syst. Bot.</source> <volume>32</volume>, <fpage>81</fpage>&#x2013;<lpage>92</lpage>. doi: <pub-id pub-id-type="doi">10.1600/036364407780360265</pub-id>
</citation>
</ref>
<ref id="B64">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Shen</surname> <given-names>T.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>Flavonoids from the leaves of Epimedium Koreanum Nakai and their potential cytotoxic activities</article-title>. <source>Nat. Prod. Res.</source> <volume>34</volume>, <fpage>1256</fpage>&#x2013;<lpage>1263</lpage>. doi: <pub-id pub-id-type="doi">10.1080/14786419.2018.1560283</pub-id>
</citation>
</ref>
<ref id="B65">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhong</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Shi</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Zhong</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Xia</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>J.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>The potential of Epimedium koreanum Nakai for herb-drug interaction</article-title>. <source>J. Pharm. Pharmacol.</source> <volume>69</volume>, <fpage>1398</fpage>&#x2013;<lpage>1408</lpage>. doi: <pub-id pub-id-type="doi">10.1111/jphp.12773</pub-id>
</citation>
</ref>
<ref id="B66">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhu</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Shi</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Jiang</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Jiao</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Zhu</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>R.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>Investigation of the mechanisms of chuankezhi injection in the treatment of asthma based on the network pharmacology approach</article-title>. <source>Evid. Based Complement. Altern. Med.</source> <volume>2021</volume>, <fpage>5517041</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1155/2021/5517041</pub-id>
</citation>
</ref>
</ref-list>
</back>
</article>