Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice.
Identifieur interne : 001B24 ( Main/Corpus ); précédent : 001B23; suivant : 001B25Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice.
Auteurs : Yiyi Wang ; Lin Feng ; Yuxin Zhu ; Yuan Li ; Hanwei Yan ; Yan XiangSource :
- Biology direct [ 1745-6150 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
Abstract
BACKGROUND
WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots).
RESULTS
In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns.
CONCLUSIONS
This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.
DOI: 10.1186/s13062-015-0076-3
PubMed: 26350041
PubMed Central: PMC4563840
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Adelyn@foxmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Zhu, Yuxin" sort="Zhu, Yuxin" uniqKey="Zhu Y" first="Yuxin" last="Zhu">Yuxin Zhu</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. yxz@ahau.edu.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Yuan" sort="Li, Yuan" uniqKey="Li Y" first="Yuan" last="Li">Yuan Li</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Lyuan@ahau.edu.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Yan, Hanwei" sort="Yan, Hanwei" uniqKey="Yan H" first="Hanwei" last="Yan">Hanwei Yan</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. hwyanahau@163.com.</nlm:affiliation></affiliation></author><author><name sortKey="Xiang, Yan" sort="Xiang, Yan" uniqKey="Xiang Y" first="Yan" last="Xiang">Yan Xiang</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau@sina.com.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, 230036, China. xiangyanahau@sina.com.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26350041</idno><idno type="pmid">26350041</idno><idno type="doi">10.1186/s13062-015-0076-3</idno><idno type="pmc">PMC4563840</idno><idno type="wicri:Area/Main/Corpus">001B24</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001B24</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice.</title><author><name sortKey="Wang, Yiyi" sort="Wang, Yiyi" uniqKey="Wang Y" first="Yiyi" last="Wang">Yiyi Wang</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. yywahaq@sina.com.</nlm:affiliation></affiliation></author><author><name sortKey="Feng, Lin" sort="Feng, Lin" uniqKey="Feng L" first="Lin" last="Feng">Lin Feng</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Adelyn@foxmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Zhu, Yuxin" sort="Zhu, Yuxin" uniqKey="Zhu Y" first="Yuxin" last="Zhu">Yuxin Zhu</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. yxz@ahau.edu.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Yuan" sort="Li, Yuan" uniqKey="Li Y" first="Yuan" last="Li">Yuan Li</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Lyuan@ahau.edu.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Yan, Hanwei" sort="Yan, Hanwei" uniqKey="Yan H" first="Hanwei" last="Yan">Hanwei Yan</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. hwyanahau@163.com.</nlm:affiliation></affiliation></author><author><name sortKey="Xiang, Yan" sort="Xiang, Yan" uniqKey="Xiang Y" first="Yan" last="Xiang">Yan Xiang</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau@sina.com.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, 230036, China. xiangyanahau@sina.com.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Biology direct</title><idno type="eISSN">1745-6150</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Magnoliopsida (genetics)</term><term>Multigene Family (MeSH)</term><term>Oryza (genetics)</term><term>Phylogeny (MeSH)</term><term>Populus (genetics)</term><term>Vitis (genetics)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Magnoliopsida</term><term>Oryza</term><term>Populus</term><term>Vitis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Multigene Family</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots).</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26350041</PMID><DateCompleted><Year>2016</Year><Month>06</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1745-6150</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><PubDate><Year>2015</Year><Month>Sep</Month><Day>08</Day></PubDate></JournalIssue><Title>Biology direct</Title><ISOAbbreviation>Biol Direct</ISOAbbreviation></Journal><ArticleTitle>Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice.</ArticleTitle><Pagination><MedlinePgn>48</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13062-015-0076-3</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots).</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yiyi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. yywahaq@sina.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Lin</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Adelyn@foxmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Yuxin</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. yxz@ahau.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yuan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. 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