Gene duplication and fragment recombination drive functional diversification of a superfamily of cytoplasmic effectors in Phytophthora sojae.
Identifieur interne : 001237 ( Main/Corpus ); précédent : 001236; suivant : 001238Gene duplication and fragment recombination drive functional diversification of a superfamily of cytoplasmic effectors in Phytophthora sojae.
Auteurs : Danyu Shen ; Tingli Liu ; Wenwu Ye ; Li Liu ; Peihan Liu ; Yuren Wu ; Yuanchao Wang ; Daolong DouSource :
- PloS one [ 1932-6203 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
- classification : Phytophthora.
- genetics : Gene Duplication, Phytophthora.
- Biological Evolution.
Abstract
Phytophthora and other oomycetes secrete a large number of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling and necrosis inducing proteins (CRN), or Crinkler. Here, we first investigated the evolutionary patterns and mechanisms of CRN effectors in Phytophthora sojae and compared them to two other Phytophthora species. The genes encoding CRN effectors could be divided into 45 orthologous gene groups (OGG), and most OGGs unequally distributed in the three species, in which each underwent large number of gene gains or losses, indicating that the CRN genes expanded after species evolution in Phytophthora and evolved through pathoadaptation. The 134 expanded genes in P. sojae encoded family proteins including 82 functional genes and expressed at higher levels while the other 68 genes encoding orphan proteins were less expressed and contained 50 pseudogenes. Furthermore, we demonstrated that most expanded genes underwent gene duplication or/and fragment recombination. Three different mechanisms that drove gene duplication or recombination were identified. Finally, the expanded CRN effectors exhibited varying pathogenic functions, including induction of programmed cell death (PCD) and suppression of PCD through PAMP-triggered immunity or/and effector-triggered immunity. Overall, these results suggest that gene duplication and fragment recombination may be two mechanisms that drive the expansion and neofunctionalization of the CRN family in P. sojae, which aids in understanding the roles of CRN effectors within each oomycete pathogen.
DOI: 10.1371/journal.pone.0070036
PubMed: 23922898
PubMed Central: PMC3726527
Links to Exploration step
pubmed:23922898Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Gene duplication and fragment recombination drive functional diversification of a superfamily of cytoplasmic effectors in Phytophthora sojae.</title><author><name sortKey="Shen, Danyu" sort="Shen, Danyu" uniqKey="Shen D" first="Danyu" last="Shen">Danyu Shen</name><affiliation><nlm:affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Tingli" sort="Liu, Tingli" uniqKey="Liu T" first="Tingli" last="Liu">Tingli Liu</name></author><author><name sortKey="Ye, Wenwu" sort="Ye, Wenwu" uniqKey="Ye W" first="Wenwu" last="Ye">Wenwu Ye</name></author><author><name sortKey="Liu, Li" sort="Liu, Li" uniqKey="Liu L" first="Li" last="Liu">Li Liu</name></author><author><name sortKey="Liu, Peihan" sort="Liu, Peihan" uniqKey="Liu P" first="Peihan" last="Liu">Peihan Liu</name></author><author><name sortKey="Wu, Yuren" sort="Wu, Yuren" uniqKey="Wu Y" first="Yuren" last="Wu">Yuren Wu</name></author><author><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name></author><author><name sortKey="Dou, Daolong" sort="Dou, Daolong" uniqKey="Dou D" first="Daolong" last="Dou">Daolong Dou</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23922898</idno><idno type="pmid">23922898</idno><idno type="doi">10.1371/journal.pone.0070036</idno><idno type="pmc">PMC3726527</idno><idno type="wicri:Area/Main/Corpus">001237</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001237</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Gene duplication and fragment recombination drive functional diversification of a superfamily of cytoplasmic effectors in Phytophthora sojae.</title><author><name sortKey="Shen, Danyu" sort="Shen, Danyu" uniqKey="Shen D" first="Danyu" last="Shen">Danyu Shen</name><affiliation><nlm:affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Tingli" sort="Liu, Tingli" uniqKey="Liu T" first="Tingli" last="Liu">Tingli Liu</name></author><author><name sortKey="Ye, Wenwu" sort="Ye, Wenwu" uniqKey="Ye W" first="Wenwu" last="Ye">Wenwu Ye</name></author><author><name sortKey="Liu, Li" sort="Liu, Li" uniqKey="Liu L" first="Li" last="Liu">Li Liu</name></author><author><name sortKey="Liu, Peihan" sort="Liu, Peihan" uniqKey="Liu P" first="Peihan" last="Liu">Peihan Liu</name></author><author><name sortKey="Wu, Yuren" sort="Wu, Yuren" uniqKey="Wu Y" first="Yuren" last="Wu">Yuren Wu</name></author><author><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name></author><author><name sortKey="Dou, Daolong" sort="Dou, Daolong" uniqKey="Dou D" first="Daolong" last="Dou">Daolong Dou</name></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biological Evolution (MeSH)</term><term>Gene Duplication (genetics)</term><term>Phytophthora (classification)</term><term>Phytophthora (genetics)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gene Duplication</term><term>Phytophthora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biological Evolution</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Phytophthora and other oomycetes secrete a large number of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling and necrosis inducing proteins (CRN), or Crinkler. Here, we first investigated the evolutionary patterns and mechanisms of CRN effectors in Phytophthora sojae and compared them to two other Phytophthora species. The genes encoding CRN effectors could be divided into 45 orthologous gene groups (OGG), and most OGGs unequally distributed in the three species, in which each underwent large number of gene gains or losses, indicating that the CRN genes expanded after species evolution in Phytophthora and evolved through pathoadaptation. The 134 expanded genes in P. sojae encoded family proteins including 82 functional genes and expressed at higher levels while the other 68 genes encoding orphan proteins were less expressed and contained 50 pseudogenes. Furthermore, we demonstrated that most expanded genes underwent gene duplication or/and fragment recombination. Three different mechanisms that drove gene duplication or recombination were identified. Finally, the expanded CRN effectors exhibited varying pathogenic functions, including induction of programmed cell death (PCD) and suppression of PCD through PAMP-triggered immunity or/and effector-triggered immunity. Overall, these results suggest that gene duplication and fragment recombination may be two mechanisms that drive the expansion and neofunctionalization of the CRN family in P. sojae, which aids in understanding the roles of CRN effectors within each oomycete pathogen. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23922898</PMID><DateCompleted><Year>2014</Year><Month>03</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-Print"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>7</Issue><PubDate><Year>2013</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Gene duplication and fragment recombination drive functional diversification of a superfamily of cytoplasmic effectors in Phytophthora sojae.</ArticleTitle><Pagination><MedlinePgn>e70036</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0070036</ELocationID><Abstract><AbstractText>Phytophthora and other oomycetes secrete a large number of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling and necrosis inducing proteins (CRN), or Crinkler. Here, we first investigated the evolutionary patterns and mechanisms of CRN effectors in Phytophthora sojae and compared them to two other Phytophthora species. The genes encoding CRN effectors could be divided into 45 orthologous gene groups (OGG), and most OGGs unequally distributed in the three species, in which each underwent large number of gene gains or losses, indicating that the CRN genes expanded after species evolution in Phytophthora and evolved through pathoadaptation. The 134 expanded genes in P. sojae encoded family proteins including 82 functional genes and expressed at higher levels while the other 68 genes encoding orphan proteins were less expressed and contained 50 pseudogenes. Furthermore, we demonstrated that most expanded genes underwent gene duplication or/and fragment recombination. Three different mechanisms that drove gene duplication or recombination were identified. Finally, the expanded CRN effectors exhibited varying pathogenic functions, including induction of programmed cell death (PCD) and suppression of PCD through PAMP-triggered immunity or/and effector-triggered immunity. Overall, these results suggest that gene duplication and fragment recombination may be two mechanisms that drive the expansion and neofunctionalization of the CRN family in P. sojae, which aids in understanding the roles of CRN effectors within each oomycete pathogen. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Danyu</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Tingli</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Wenwu</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Li</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Peihan</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Yuren</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yuanchao</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Dou</LastName><ForeName>Daolong</ForeName><Initials>D</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>2013</Year><Month>07</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005075" MajorTopicYN="N">Biological Evolution</DescriptorName></MeshHeading><MeshHeading><DescriptorName 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