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A high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes

hal.structure.identifierSanté et agroécologie du vignoble [UMR SAVE]
dc.contributor.authorDUSSERT, Yann
hal.structure.identifierSanté et agroécologie du vignoble [UMR SAVE]
dc.contributor.authorMAZET, Isabelle D.
hal.structure.identifierSanté et agroécologie du vignoble [UMR SAVE]
dc.contributor.authorCOUTURE, Carole
hal.structure.identifierLaboratoire des interactions plantes micro-organismes [LIPM]
dc.contributor.authorGOUZY, Jerome
hal.structure.identifierSanté de la vigne et qualité du vin [SVQV]
dc.contributor.authorPIRON, Marie-Christine
hal.structure.identifierGénome et Transcriptome - Plateforme Génomique [GeT-PlaGe]
dc.contributor.authorKUCHLY, Claire
hal.structure.identifierGénome et Transcriptome - Plateforme Génomique [GeT-PlaGe]
dc.contributor.authorBOUCHEZ, Olivier
hal.structure.identifierBiologie, Epidémiologie et analyse de risque en Santé Animale [BIOEPAR]
dc.contributor.authorRISPE, Claude
hal.structure.identifierSanté de la vigne et qualité du vin [SVQV]
dc.contributor.authorMESTRE, Pere
hal.structure.identifierSanté et agroécologie du vignoble [UMR SAVE]
dc.contributor.authorDELMOTTE, François
dc.date.accessioned2024-04-08T12:33:57Z
dc.date.available2024-04-08T12:33:57Z
dc.date.issued2019
dc.identifier.issn1759-6653
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/197233
dc.description.abstractEnDowny 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.
dc.language.isoen
dc.publisherSociety for Molecular Biology and Evolution
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectPlasmopara viticola
dc.subject.enPacBio
dc.subject.enlong reads
dc.subject.enoomycete
dc.subject.enplant–pathogen interactions
dc.title.enA high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes
dc.typeArticle de revue
dc.identifier.doi10.1093/gbe/evz048
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences de l'environnement
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences du Vivant [q-bio]/Génétique
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique animale
bordeaux.journalGenome Biology and Evolution
bordeaux.page954-969
bordeaux.volume11
bordeaux.hal.laboratoriesSanté et Agro-Ecologie du Vignoble (SAVE) - UMR 1065*
bordeaux.issue3
bordeaux.institutionBordeaux Sciences Agro
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-02628726
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02628726v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Genome%20Biology%20and%20Evolution&rft.date=2019&rft.volume=11&rft.issue=3&rft.spage=954-969&rft.epage=954-969&rft.eissn=1759-6653&rft.issn=1759-6653&rft.au=DUSSERT,%20Yann&MAZET,%20Isabelle%20D.&COUTURE,%20Carole&GOUZY,%20Jerome&PIRON,%20Marie-Christine&rft.genre=article


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