Comparative Genomic Analysis among Four Representative Isolates of Phytophthora sojae Reveals Genes under Evolutionary Selection.
Identifieur interne : 000C88 ( Main/Exploration ); précédent : 000C87; suivant : 000C89Comparative Genomic Analysis among Four Representative Isolates of Phytophthora sojae Reveals Genes under Evolutionary Selection.
Auteurs : Wenwu Ye [République populaire de Chine] ; Yang Wang [République populaire de Chine] ; Brett M. Tyler [États-Unis] ; Yuanchao Wang [République populaire de Chine]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2016.
Abstract
Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative P. sojae isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in P. sojae and will provide clues for identification of new virulence factors in the oomycete plant pathogens.
DOI: 10.3389/fmicb.2016.01547
PubMed: 27746768
PubMed Central: PMC5042962
Affiliations:
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Tyler</name><affiliation wicri:level="1"><nlm:affiliation>Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis OR, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis OR</wicri:regionArea><wicri:noRegion>Corvallis OR</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, Nanjing Agricultural University Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Plant Pathology, Nanjing Agricultural University Nanjing</wicri:regionArea><wicri:noRegion>Nanjing Agricultural University Nanjing</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In <i>Phytophthora sojae</i>, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of <i>P. sojae</i>, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative <i>P. sojae</i> isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in <i>P. sojae</i> and will provide clues for identification of new virulence factors in the oomycete plant pathogens.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27746768</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>Comparative Genomic Analysis among Four Representative Isolates of <i>Phytophthora sojae</i> Reveals Genes under Evolutionary Selection.</ArticleTitle><Pagination><MedlinePgn>1547</MedlinePgn></Pagination><Abstract><AbstractText>Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In <i>Phytophthora sojae</i>, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of <i>P. sojae</i>, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative <i>P. sojae</i> isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in <i>P. sojae</i> and will provide clues for identification of new virulence factors in the oomycete plant pathogens.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Wenwu</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tyler</LastName><ForeName>Brett M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis OR, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yuanchao</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>09</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Microbiol</MedlineTA><NlmUniqueID>101548977</NlmUniqueID><ISSNLinking>1664-302X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora</Keyword><Keyword MajorTopicYN="N">comparative genomic analysis</Keyword><Keyword MajorTopicYN="N">effectors</Keyword><Keyword MajorTopicYN="N">evolution</Keyword><Keyword MajorTopicYN="N">positive 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