Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors.
Identifieur interne : 000105 ( Main/Exploration ); précédent : 000104; suivant : 000106Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors.
Auteurs : Jana Sperschneider [Australie] ; Hua Ying [Australie] ; Peter N. Dodds [Australie] ; Donald M. Gardiner [Australie] ; Narayana M. Upadhyaya [Australie] ; Karam B. Singh [Australie] ; John M. Manners [Australie] ; Jennifer M. Taylor [Australie]Source :
- Frontiers in plant science [ 1664-462X ] ; 2014.
Abstract
Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control.
DOI: 10.3389/fpls.2014.00372
PubMed: 25225496
PubMed Central: PMC4150398
Affiliations:
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Manners</name><affiliation wicri:level="1"><nlm:affiliation>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Taylor, Jennifer M" sort="Taylor, Jennifer M" uniqKey="Taylor J" first="Jennifer M" last="Taylor">Jennifer M. Taylor</name><affiliation wicri:level="1"><nlm:affiliation>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25225496</PMID><DateCompleted><Year>2014</Year><Month>09</Month><Day>16</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors.</ArticleTitle><Pagination><MedlinePgn>372</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2014.00372</ELocationID><Abstract><AbstractText>Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sperschneider</LastName><ForeName>Jana</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Plant Industry, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation Perth, WA, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ying</LastName><ForeName>Hua</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dodds</LastName><ForeName>Peter N</ForeName><Initials>PN</Initials><AffiliationInfo><Affiliation>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gardiner</LastName><ForeName>Donald M</ForeName><Initials>DM</Initials><AffiliationInfo><Affiliation>Plant Industry, Queensland Bioscience Precinct, Commonwealth Scientific and Industrial Research Organisation Brisbane, QLD, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Upadhyaya</LastName><ForeName>Narayana M</ForeName><Initials>NM</Initials><AffiliationInfo><Affiliation>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Karam B</ForeName><Initials>KB</Initials><AffiliationInfo><Affiliation>Plant Industry, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation Perth, WA, Australia ; University of Western Australia Institute of Agriculture, University of Western Australia Crawley, WA, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Manners</LastName><ForeName>John M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>Jennifer M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Plant Industry, Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>09</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Puccinia graminis</Keyword><Keyword MajorTopicYN="N">adaptation</Keyword><Keyword MajorTopicYN="N">avirulence</Keyword><Keyword MajorTopicYN="N">effector</Keyword><Keyword MajorTopicYN="N">fungal pathogens</Keyword><Keyword MajorTopicYN="N">rust</Keyword><Keyword MajorTopicYN="N">selection</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>05</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>07</Month><Day>11</Day></PubMedPubDate><PubMedPubDate 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Dodds</name><name sortKey="Gardiner, Donald M" sort="Gardiner, Donald M" uniqKey="Gardiner D" first="Donald M" last="Gardiner">Donald M. Gardiner</name><name sortKey="Manners, John M" sort="Manners, John M" uniqKey="Manners J" first="John M" last="Manners">John M. Manners</name><name sortKey="Singh, Karam B" sort="Singh, Karam B" uniqKey="Singh K" first="Karam B" last="Singh">Karam B. Singh</name><name sortKey="Taylor, Jennifer M" sort="Taylor, Jennifer M" uniqKey="Taylor J" first="Jennifer M" last="Taylor">Jennifer M. Taylor</name><name sortKey="Upadhyaya, Narayana M" sort="Upadhyaya, Narayana M" uniqKey="Upadhyaya N" first="Narayana M" last="Upadhyaya">Narayana M. Upadhyaya</name><name sortKey="Ying, Hua" sort="Ying, Hua" uniqKey="Ying H" first="Hua" last="Ying">Hua Ying</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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