Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots.
Identifieur interne : 000F10 ( Main/Exploration ); précédent : 000F09; suivant : 000F11Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots.
Auteurs : Xing Liu [République populaire de Chine] ; Zhichao Sun [République populaire de Chine] ; Wei Dong [République populaire de Chine] ; Zhengjia Wang [République populaire de Chine] ; Liangsheng Zhang [République populaire de Chine]Source :
- Genome biology and evolution [ 1759-6653 ] ; 2018.
Descripteurs français
- KwdFr :
- Arabidopsis (MeSH), Duplication de gène (MeSH), Expression des gènes (MeSH), Facteurs de transcription (génétique), Famille multigénique (MeSH), Magnoliopsida (génétique), Phylogenèse (MeSH), Protéines d'Arabidopsis (génétique), Sélection génétique (MeSH), Éléments de régulation transcriptionnelle (MeSH), Évolution moléculaire (MeSH).
- MESH :
English descriptors
- KwdEn :
- Arabidopsis (MeSH), Arabidopsis Proteins (genetics), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Gene Expression (MeSH), Magnoliopsida (genetics), Multigene Family (MeSH), Phylogeny (MeSH), Regulatory Elements, Transcriptional (MeSH), Selection, Genetic (MeSH), Transcription Factors (genetics).
- MESH :
- chemical , genetics : Arabidopsis Proteins, Transcription Factors.
- genetics : Magnoliopsida.
- Arabidopsis, Evolution, Molecular, Gene Duplication, Gene Expression, Multigene Family, Phylogeny, Regulatory Elements, Transcriptional, Selection, Genetic.
Abstract
SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that regulates vital developmental processes in plants. In Arabidopsis, there are two SVP paralogs, SVP/AGAMOUS-LIKE22 (SVP/AGL22) and AGL24. SVP protein suppresses the flowering process, whereas AGL24 acts as a flowering activator. Phylogenetic analysis of SVP genes representing most of the sequenced eudicot species showed that the SVP gene family could be divided into three major clades in eudicots (SVP1, SVP2, and SVP3), most likely resulting from an ancient whole-genome triplication in core eudicots. Among them, the SVP1 (SVP) and SVP2 (AGL24) clades are retained in nearly all species, whereas the SVP3 clade has been lost in Brassicaceae, Myrtaceae, and some species in other families. Reflecting lineage-specific tandem duplication and whole-genome duplication, SVP gene copy numbers ranged from 3 to 11 in the analyzed species. Sequence analysis showed that SVP3 proteins have obvious differences with SVP1 and SVP2 in the C-terminal (C) domain and intervening (I) domain. Positive selection analysis also showed that the ω (dN/dS) value was highest in the SVP3 clade, with 17 positive selection sites detected in the SVP3 clade. Promoter analysis for cis-regulatory elements showed that some genes in the SVP2 and SVP3 clades may be regulated by abscisic acid, ethylene, and gibberellin. RNA-seq data from grape, poplar, and apple revealed that genes in SVP3 group are highly expressed in vegetative organs such as buds, leaves, cotyledons, and dormant buds in particular, indicating the involvement of genes belong to SVP3 group in the dormancy process. Overall, the findings underscore the functional diversity of the SVP genes in eudicots.
DOI: 10.1093/gbe/evy235
PubMed: 30364940
PubMed Central: PMC6251477
Affiliations:
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Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou</wicri:regionArea><placeName><settlement type="city">Fuzhou</settlement><region type="province">Fujian</region></placeName></affiliation></author><author><name sortKey="Sun, Zhichao" sort="Sun, Zhichao" uniqKey="Sun Z" first="Zhichao" last="Sun">Zhichao Sun</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Dong, Wei" sort="Dong, Wei" uniqKey="Dong W" first="Wei" last="Dong">Wei Dong</name><affiliation wicri:level="3"><nlm:affiliation>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou</wicri:regionArea><placeName><settlement type="city">Fuzhou</settlement><region type="province">Fujian</region></placeName></affiliation></author><author><name sortKey="Wang, Zhengjia" sort="Wang, Zhengjia" uniqKey="Wang Z" first="Zhengjia" last="Wang">Zhengjia Wang</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Zhang, Liangsheng" sort="Zhang, Liangsheng" uniqKey="Zhang L" first="Liangsheng" last="Zhang">Liangsheng Zhang</name><affiliation wicri:level="3"><nlm:affiliation>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou</wicri:regionArea><placeName><settlement type="city">Fuzhou</settlement><region type="province">Fujian</region></placeName></affiliation></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (MeSH)</term><term>Arabidopsis Proteins (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Expression (MeSH)</term><term>Magnoliopsida (genetics)</term><term>Multigene Family (MeSH)</term><term>Phylogeny (MeSH)</term><term>Regulatory Elements, Transcriptional (MeSH)</term><term>Selection, Genetic (MeSH)</term><term>Transcription Factors (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (MeSH)</term><term>Duplication de gène (MeSH)</term><term>Expression des gènes (MeSH)</term><term>Facteurs de transcription (génétique)</term><term>Famille multigénique (MeSH)</term><term>Magnoliopsida (génétique)</term><term>Phylogenèse (MeSH)</term><term>Protéines d'Arabidopsis (génétique)</term><term>Sélection génétique (MeSH)</term><term>Éléments de régulation transcriptionnelle (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Arabidopsis Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Facteurs de transcription</term><term>Magnoliopsida</term><term>Protéines d'Arabidopsis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Arabidopsis</term><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Gene Expression</term><term>Multigene Family</term><term>Phylogeny</term><term>Regulatory Elements, Transcriptional</term><term>Selection, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Arabidopsis</term><term>Duplication de gène</term><term>Expression des gènes</term><term>Famille multigénique</term><term>Phylogenèse</term><term>Sélection génétique</term><term>Éléments de régulation transcriptionnelle</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that regulates vital developmental processes in plants. In Arabidopsis, there are two SVP paralogs, SVP/AGAMOUS-LIKE22 (SVP/AGL22) and AGL24. SVP protein suppresses the flowering process, whereas AGL24 acts as a flowering activator. Phylogenetic analysis of SVP genes representing most of the sequenced eudicot species showed that the SVP gene family could be divided into three major clades in eudicots (SVP1, SVP2, and SVP3), most likely resulting from an ancient whole-genome triplication in core eudicots. Among them, the SVP1 (SVP) and SVP2 (AGL24) clades are retained in nearly all species, whereas the SVP3 clade has been lost in Brassicaceae, Myrtaceae, and some species in other families. Reflecting lineage-specific tandem duplication and whole-genome duplication, SVP gene copy numbers ranged from 3 to 11 in the analyzed species. Sequence analysis showed that SVP3 proteins have obvious differences with SVP1 and SVP2 in the C-terminal (C) domain and intervening (I) domain. Positive selection analysis also showed that the ω (dN/dS) value was highest in the SVP3 clade, with 17 positive selection sites detected in the SVP3 clade. Promoter analysis for cis-regulatory elements showed that some genes in the SVP2 and SVP3 clades may be regulated by abscisic acid, ethylene, and gibberellin. RNA-seq data from grape, poplar, and apple revealed that genes in SVP3 group are highly expressed in vegetative organs such as buds, leaves, cotyledons, and dormant buds in particular, indicating the involvement of genes belong to SVP3 group in the dormancy process. Overall, the findings underscore the functional diversity of the SVP genes in eudicots.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30364940</PMID><DateCompleted><Year>2019</Year><Month>02</Month><Day>22</Day></DateCompleted><DateRevised><Year>2019</Year><Month>02</Month><Day>22</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>11</Issue><PubDate><Year>2018</Year><Month>11</Month><Day>01</Day></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots.</ArticleTitle><Pagination><MedlinePgn>3026-3037</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evy235</ELocationID><Abstract><AbstractText>SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that regulates vital developmental processes in plants. In Arabidopsis, there are two SVP paralogs, SVP/AGAMOUS-LIKE22 (SVP/AGL22) and AGL24. SVP protein suppresses the flowering process, whereas AGL24 acts as a flowering activator. Phylogenetic analysis of SVP genes representing most of the sequenced eudicot species showed that the SVP gene family could be divided into three major clades in eudicots (SVP1, SVP2, and SVP3), most likely resulting from an ancient whole-genome triplication in core eudicots. Among them, the SVP1 (SVP) and SVP2 (AGL24) clades are retained in nearly all species, whereas the SVP3 clade has been lost in Brassicaceae, Myrtaceae, and some species in other families. Reflecting lineage-specific tandem duplication and whole-genome duplication, SVP gene copy numbers ranged from 3 to 11 in the analyzed species. Sequence analysis showed that SVP3 proteins have obvious differences with SVP1 and SVP2 in the C-terminal (C) domain and intervening (I) domain. Positive selection analysis also showed that the ω (dN/dS) value was highest in the SVP3 clade, with 17 positive selection sites detected in the SVP3 clade. Promoter analysis for cis-regulatory elements showed that some genes in the SVP2 and SVP3 clades may be regulated by abscisic acid, ethylene, and gibberellin. RNA-seq data from grape, poplar, and apple revealed that genes in SVP3 group are highly expressed in vegetative organs such as buds, leaves, cotyledons, and dormant buds in particular, indicating the involvement of genes belong to SVP3 group in the dormancy process. Overall, the findings underscore the functional diversity of the SVP genes in eudicots.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Xing</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Zhichao</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dong</LastName><ForeName>Wei</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zhengjia</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Liangsheng</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Center for Genomics and Biotechnology; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Life Science; Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>11</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol Evol</MedlineTA><NlmUniqueID>101509707</NlmUniqueID><ISSNLinking>1759-6653</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029681">Arabidopsis 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sort="Dong, Wei" uniqKey="Dong W" first="Wei" last="Dong">Wei Dong</name><name sortKey="Sun, Zhichao" sort="Sun, Zhichao" uniqKey="Sun Z" first="Zhichao" last="Sun">Zhichao Sun</name><name sortKey="Wang, Zhengjia" sort="Wang, Zhengjia" uniqKey="Wang Z" first="Zhengjia" last="Wang">Zhengjia Wang</name><name sortKey="Zhang, Liangsheng" sort="Zhang, Liangsheng" uniqKey="Zhang L" first="Liangsheng" last="Zhang">Liangsheng Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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