Recent duplications dominate NBS-encoding gene expansion in two woody species.
Identifieur interne : 003857 ( Main/Corpus ); précédent : 003856; suivant : 003858Recent duplications dominate NBS-encoding gene expansion in two woody species.
Auteurs : Sihai Yang ; Xiaohui Zhang ; Jia-Xing Yue ; Dacheng Tian ; Jian-Qun ChenSource :
- Molecular genetics and genomics : MGG [ 1617-4615 ] ; 2008.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Plant Proteins.
- genetics : Chromosomes, Plant, Plant Proteins, Populus, Vitis, Wood.
- Evolution, Molecular, Gene Conversion, Gene Duplication, Genes, Plant, Phylogeny, Protein Structure, Tertiary.
Abstract
Most disease resistance genes in plants encode NBS-LRR proteins. However, in woody species, little is known about the evolutionary history of these genes. Here, we identified 459 and 330 respective NBS-LRRs in grapevine and poplar genomes. We subsequently investigated protein motif composition, phylogenetic relationships and physical locations. We found significant excesses of recent duplications in perennial species, compared with those of annuals, represented by rice and Arabidopsis. Consequently, we observed higher nucleotide identity among paralogs and a higher percentage of NBS-encoding genes positioned in numerous clusters in the grapevine and poplar. These results suggested that recent tandem duplication played a major role in NBS-encoding gene expansion in perennial species. These duplication events, together with a higher probability of recombination revealed in this study, could compensate for the longer generation time in woody perennial species e.g. duplication and recombination could serve to generate novel resistance specificities. In addition, we observed extensive species-specific expansion in TIR-NBS-encoding genes. Non-TIR-NBS-encoding genes were poly- or paraphyletic, i.e. genes from three or more plant species were nested in different clades, suggesting different evolutionary patterns between these two gene types.
DOI: 10.1007/s00438-008-0355-0
PubMed: 18563445
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Recent duplications dominate NBS-encoding gene expansion in two woody species.</title><author><name sortKey="Yang, Sihai" sort="Yang, Sihai" uniqKey="Yang S" first="Sihai" last="Yang">Sihai Yang</name><affiliation><nlm:affiliation>State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Xiaohui" sort="Zhang, Xiaohui" uniqKey="Zhang X" first="Xiaohui" last="Zhang">Xiaohui Zhang</name></author><author><name sortKey="Yue, Jia Xing" sort="Yue, Jia Xing" uniqKey="Yue J" first="Jia-Xing" last="Yue">Jia-Xing Yue</name></author><author><name sortKey="Tian, Dacheng" sort="Tian, Dacheng" uniqKey="Tian D" first="Dacheng" last="Tian">Dacheng Tian</name></author><author><name sortKey="Chen, Jian Qun" sort="Chen, Jian Qun" uniqKey="Chen J" first="Jian-Qun" last="Chen">Jian-Qun Chen</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18563445</idno><idno type="pmid">18563445</idno><idno type="doi">10.1007/s00438-008-0355-0</idno><idno type="wicri:Area/Main/Corpus">003857</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003857</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Recent duplications dominate NBS-encoding gene expansion in two woody species.</title><author><name sortKey="Yang, Sihai" sort="Yang, Sihai" uniqKey="Yang S" first="Sihai" last="Yang">Sihai Yang</name><affiliation><nlm:affiliation>State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Xiaohui" sort="Zhang, Xiaohui" uniqKey="Zhang X" first="Xiaohui" last="Zhang">Xiaohui Zhang</name></author><author><name sortKey="Yue, Jia Xing" sort="Yue, Jia Xing" uniqKey="Yue J" first="Jia-Xing" last="Yue">Jia-Xing Yue</name></author><author><name sortKey="Tian, Dacheng" sort="Tian, Dacheng" uniqKey="Tian D" first="Dacheng" last="Tian">Dacheng Tian</name></author><author><name sortKey="Chen, Jian Qun" sort="Chen, Jian Qun" uniqKey="Chen J" first="Jian-Qun" last="Chen">Jian-Qun Chen</name></author></analytic><series><title level="j">Molecular genetics and genomics : MGG</title><idno type="ISSN">1617-4615</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Conversion (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (genetics)</term><term>Populus (genetics)</term><term>Protein Structure, Tertiary (MeSH)</term><term>Vitis (genetics)</term><term>Wood (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Plant</term><term>Plant Proteins</term><term>Populus</term><term>Vitis</term><term>Wood</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Conversion</term><term>Gene Duplication</term><term>Genes, Plant</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Most disease resistance genes in plants encode NBS-LRR proteins. However, in woody species, little is known about the evolutionary history of these genes. Here, we identified 459 and 330 respective NBS-LRRs in grapevine and poplar genomes. We subsequently investigated protein motif composition, phylogenetic relationships and physical locations. We found significant excesses of recent duplications in perennial species, compared with those of annuals, represented by rice and Arabidopsis. Consequently, we observed higher nucleotide identity among paralogs and a higher percentage of NBS-encoding genes positioned in numerous clusters in the grapevine and poplar. These results suggested that recent tandem duplication played a major role in NBS-encoding gene expansion in perennial species. These duplication events, together with a higher probability of recombination revealed in this study, could compensate for the longer generation time in woody perennial species e.g. duplication and recombination could serve to generate novel resistance specificities. In addition, we observed extensive species-specific expansion in TIR-NBS-encoding genes. Non-TIR-NBS-encoding genes were poly- or paraphyletic, i.e. genes from three or more plant species were nested in different clades, suggesting different evolutionary patterns between these two gene types.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18563445</PMID><DateCompleted><Year>2008</Year><Month>11</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1617-4615</ISSN><JournalIssue CitedMedium="Print"><Volume>280</Volume><Issue>3</Issue><PubDate><Year>2008</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Molecular genetics and genomics : MGG</Title><ISOAbbreviation>Mol Genet Genomics</ISOAbbreviation></Journal><ArticleTitle>Recent duplications dominate NBS-encoding gene expansion in two woody species.</ArticleTitle><Pagination><MedlinePgn>187-98</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00438-008-0355-0</ELocationID><Abstract><AbstractText>Most disease resistance genes in plants encode NBS-LRR proteins. However, in woody species, little is known about the evolutionary history of these genes. Here, we identified 459 and 330 respective NBS-LRRs in grapevine and poplar genomes. We subsequently investigated protein motif composition, phylogenetic relationships and physical locations. We found significant excesses of recent duplications in perennial species, compared with those of annuals, represented by rice and Arabidopsis. Consequently, we observed higher nucleotide identity among paralogs and a higher percentage of NBS-encoding genes positioned in numerous clusters in the grapevine and poplar. These results suggested that recent tandem duplication played a major role in NBS-encoding gene expansion in perennial species. These duplication events, together with a higher probability of recombination revealed in this study, could compensate for the longer generation time in woody perennial species e.g. duplication and recombination could serve to generate novel resistance specificities. In addition, we observed extensive species-specific expansion in TIR-NBS-encoding genes. Non-TIR-NBS-encoding genes were poly- or paraphyletic, i.e. genes from three or more plant species were nested in different clades, suggesting different evolutionary patterns between these two gene types.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Sihai</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Xiaohui</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Yue</LastName><ForeName>Jia-Xing</ForeName><Initials>JX</Initials></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Dacheng</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Jian-Qun</ForeName><Initials>JQ</Initials></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>2008</Year><Month>06</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mol Genet Genomics</MedlineTA><NlmUniqueID>101093320</NlmUniqueID><ISSNLinking>1617-4623</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName><QualifierName UI="Q000235" 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