A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes.
Identifieur interne : 000204 ( Main/Exploration ); précédent : 000203; suivant : 000205A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes.
Auteurs : Yann Dussert [France] ; Isabelle D. Mazet [France] ; Carole Couture [France] ; Jérôme Gouzy [France] ; Marie-Christine Piron [France] ; Claire Kuchly [France] ; Olivier Bouchez [France] ; Claude Rispe [France] ; Pere Mestre [France] ; François Delmotte [France]Source :
- Genome biology and evolution [ 1759-6653 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Interactions hôte-pathogène, Oomycetes.
- microbiologie : Vitis.
- pathogénicité : Oomycetes.
- Adaptation biologique, Famille multigénique, Génome, Maladies des plantes, Sélection génétique, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- genetics : Host-Pathogen Interactions, Oomycetes.
- microbiology : Vitis.
- pathogenicity : Oomycetes.
- Adaptation, Biological, Evolution, Molecular, Genome, Multigene Family, Plant Diseases, Selection, Genetic.
Abstract
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
DOI: 10.1093/gbe/evz048
PubMed: 30847481
PubMed Central: PMC6660063
Affiliations:
- France
- Alsace (région administrative), Grand Est, Pays de la Loire
- Colmar, Nantes
- Université de Strasbourg
Links toward previous steps (curation, corpus...)
Le document en format XML
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type="university">Université de Strasbourg</orgName></affiliation></author><author><name sortKey="Kuchly, Claire" sort="Kuchly, Claire" uniqKey="Kuchly C" first="Claire" last="Kuchly">Claire Kuchly</name><affiliation wicri:level="1"><nlm:affiliation>US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan</wicri:regionArea><wicri:noRegion>Castanet-Tolosan</wicri:noRegion><wicri:noRegion>Castanet-Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Bouchez, Olivier" sort="Bouchez, Olivier" uniqKey="Bouchez O" first="Olivier" last="Bouchez">Olivier Bouchez</name><affiliation wicri:level="1"><nlm:affiliation>US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>US 1426 GeT-PlaGe, Genotoul, INRA, 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type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Biological (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Genome (MeSH)</term><term>Host-Pathogen Interactions (genetics)</term><term>Multigene Family (MeSH)</term><term>Oomycetes (genetics)</term><term>Oomycetes (pathogenicity)</term><term>Plant Diseases (MeSH)</term><term>Selection, Genetic (MeSH)</term><term>Vitis (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adaptation biologique (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Génome (MeSH)</term><term>Interactions hôte-pathogène (génétique)</term><term>Maladies des plantes (MeSH)</term><term>Oomycetes (génétique)</term><term>Oomycetes (pathogénicité)</term><term>Sélection génétique (MeSH)</term><term>Vitis (microbiologie)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Host-Pathogen Interactions</term><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Interactions hôte-pathogène</term><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Oomycetes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adaptation, Biological</term><term>Evolution, Molecular</term><term>Genome</term><term>Multigene Family</term><term>Plant Diseases</term><term>Selection, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adaptation biologique</term><term>Famille multigénique</term><term>Génome</term><term>Maladies des plantes</term><term>Sélection génétique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30847481</PMID><DateCompleted><Year>2019</Year><Month>06</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>3</Issue><PubDate><Year>2019</Year><Month>03</Month><Day>01</Day></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes.</ArticleTitle><Pagination><MedlinePgn>954-969</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evz048</ELocationID><Abstract><AbstractText>Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dussert</LastName><ForeName>Yann</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mazet</LastName><ForeName>Isabelle D</ForeName><Initials>ID</Initials><AffiliationInfo><Affiliation>SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Couture</LastName><ForeName>Carole</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gouzy</LastName><ForeName>Jérôme</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>LIPM, INRA, Université de Toulouse, CNRS, Castanet-Tolosan, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Piron</LastName><ForeName>Marie-Christine</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>SVQV, INRA, Université de Strasbourg, Colmar, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kuchly</LastName><ForeName>Claire</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bouchez</LastName><ForeName>Olivier</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rispe</LastName><ForeName>Claude</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>BIOEPAR, INRA, Oniris, Nantes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mestre</LastName><ForeName>Pere</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>SVQV, INRA, Université de Strasbourg, Colmar, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Delmotte</LastName><ForeName>François</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol Evol</MedlineTA><NlmUniqueID>101509707</NlmUniqueID><ISSNLinking>1759-6653</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000220" MajorTopicYN="N">Adaptation, Biological</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="N">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054884" MajorTopicYN="N">Host-Pathogen Interactions</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009868" MajorTopicYN="N">Oomycetes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000472" MajorTopicYN="N">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="N">Selection, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D027843" MajorTopicYN="N">Vitis</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Plasmopara viticola
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