Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum.
Identifieur interne : 000839 ( Main/Exploration ); précédent : 000838; suivant : 000840Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum.
Auteurs : Andrew D. Armitage [Royaume-Uni] ; Erik Lys E [Norvège] ; Charlotte F. Nellist [Royaume-Uni] ; Laura A. Lewis [Royaume-Uni] ; Liliana M. Cano [États-Unis, Royaume-Uni] ; Richard J. Harrison [Royaume-Uni] ; May B. Brurberg [Norvège]Source :
- PloS one [ 1932-6203 ] ; 2018.
Descripteurs français
- KwdFr :
- Amélioration des plantes (MeSH), Biologie informatique (MeSH), Fragaria (génétique), Fragaria (microbiologie), Génome fongique (génétique), Maladies des plantes (génétique), Maladies des plantes (microbiologie), Phytophthora (génétique), Phytophthora (pathogénicité), Séquençage du génome entier (MeSH).
- MESH :
- génétique : Fragaria, Génome fongique, Maladies des plantes, Phytophthora.
- microbiologie : Fragaria, Maladies des plantes.
- pathogénicité : Phytophthora.
- Amélioration des plantes, Biologie informatique, Séquençage du génome entier.
English descriptors
- KwdEn :
- MESH :
- genetics : Fragaria, Genome, Fungal, Phytophthora, Plant Diseases.
- microbiology : Fragaria, Plant Diseases.
- pathogenicity : Phytophthora.
- Computational Biology, Plant Breeding, Whole Genome Sequencing.
Abstract
The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.
DOI: 10.1371/journal.pone.0202305
PubMed: 30278048
PubMed Central: PMC6168125
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30278048</PMID><DateCompleted><Year>2019</Year><Month>03</Month><Day>06</Day></DateCompleted><DateRevised><Year>2019</Year><Month>03</Month><Day>06</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>10</Issue><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum.</ArticleTitle><Pagination><MedlinePgn>e0202305</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0202305</ELocationID><Abstract><AbstractText>The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Armitage</LastName><ForeName>Andrew D</ForeName><Initials>AD</Initials><Identifier Source="ORCID">0000-0002-0610-763X</Identifier><AffiliationInfo><Affiliation>NIAB EMR, Kent, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lysøe</LastName><ForeName>Erik</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nellist</LastName><ForeName>Charlotte F</ForeName><Initials>CF</Initials><Identifier Source="ORCID">0000-0002-7453-3710</Identifier><AffiliationInfo><Affiliation>NIAB EMR, Kent, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lewis</LastName><ForeName>Laura A</ForeName><Initials>LA</Initials><AffiliationInfo><Affiliation>NIAB EMR, Kent, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cano</LastName><ForeName>Liliana M</ForeName><Initials>LM</Initials><AffiliationInfo><Affiliation>University of Florida, UF/IFAS Indian River Research and Education Center, Fort Pierce, Florida, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>The Sainsbury Laboratory, Norwich, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Harrison</LastName><ForeName>Richard J</ForeName><Initials>RJ</Initials><Identifier Source="ORCID">0000-0002-3307-3519</Identifier><AffiliationInfo><Affiliation>NIAB EMR, Kent, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brurberg</LastName><ForeName>May B</ForeName><Initials>MB</Initials><AffiliationInfo><Affiliation>Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Norwegian University of Life Sciences (NMBU), Department of Plant Sciences, Ås, Norway.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>BB/K017071/1</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>BB/K017071/2</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><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>10</Month><Day>02</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="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031985" MajorTopicYN="N">Fragaria</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="N">Genome, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000472" MajorTopicYN="N">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000069600" MajorTopicYN="N">Plant Breeding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000073336" MajorTopicYN="Y">Whole Genome Sequencing</DescriptorName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>06</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>06</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>10</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>10</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>3</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30278048</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0202305</ArticleId><ArticleId IdType="pii">PONE-D-18-16537</ArticleId><ArticleId IdType="pmc">PMC6168125</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Breed Sci. 2012 Jan;61(5):511-22</Citation><ArticleIdList><ArticleId IdType="pubmed">23136490</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2009 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IdType="pubmed">26546319</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Norvège</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Armitage, Andrew D" sort="Armitage, Andrew D" uniqKey="Armitage A" first="Andrew D" last="Armitage">Andrew D. Armitage</name></noRegion><name sortKey="Cano, Liliana M" sort="Cano, Liliana M" uniqKey="Cano L" first="Liliana M" last="Cano">Liliana M. Cano</name><name sortKey="Harrison, Richard J" sort="Harrison, Richard J" uniqKey="Harrison R" first="Richard J" last="Harrison">Richard J. Harrison</name><name sortKey="Lewis, Laura A" sort="Lewis, Laura A" uniqKey="Lewis L" first="Laura A" last="Lewis">Laura A. Lewis</name><name sortKey="Nellist, Charlotte F" sort="Nellist, Charlotte F" uniqKey="Nellist C" first="Charlotte F" last="Nellist">Charlotte F. Nellist</name></country><country name="Norvège"><noRegion><name sortKey="Lys E, Erik" sort="Lys E, Erik" uniqKey="Lys E E" first="Erik" last="Lys E">Erik Lys E</name></noRegion><name sortKey="Brurberg, May B" sort="Brurberg, May B" uniqKey="Brurberg M" first="May B" last="Brurberg">May B. Brurberg</name><name sortKey="Brurberg, May B" sort="Brurberg, May B" uniqKey="Brurberg M" first="May B" last="Brurberg">May B. Brurberg</name></country><country name="États-Unis"><region name="Floride"><name sortKey="Cano, Liliana M" sort="Cano, Liliana M" uniqKey="Cano L" first="Liliana M" last="Cano">Liliana M. Cano</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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