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Nanopore-based detection and characterization of yam viruses.

hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorFILLOUX, Denis
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorFERNANDEZ, Emmanuel
hal.structure.identifierAnimal, Santé, Territoires, Risques et Ecosystèmes [UMR ASTRE]
dc.contributor.authorLOIRE, Etienne
hal.structure.identifierCentre de Coopération Internationale en Recherche Agronomique pour le Développement [Cirad]
dc.contributor.authorCLAUDE, Lisa
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorGALZI, Serge
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierDSMZ Plant Virus Department
dc.contributor.authorWINTER, Stephan
hal.structure.identifierICAR [ICAR]
dc.contributor.authorJEEVA, M L
hal.structure.identifierICAR [ICAR]
dc.contributor.authorMAKESHKUMAR, T
hal.structure.identifierInstitute of Infectious Diseases and Molecular Medicine [IDM]
dc.contributor.authorMARTIN, Darren P
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorROUMAGNAC, Philippe
dc.date.issued2018
dc.identifier.issn2045-2322
dc.description.abstractEnWe here assessed the capability of the MinION sequencing approach to detect and characterize viruses infecting a water yam plant. This sequencing platform consistently revealed the presence of several plant virus species, including Dioscorea bacilliform virus, Yam mild mosaic virus and Yam chlorotic necrosis virus. A potentially novel ampelovirus was also detected by a complimentary Illumina sequencing approach. The full-length genome sequence of yam chlorotic necrosis virus was determined using Sanger sequencing, which enabled determination of the coverage and sequencing accuracy of the MinION technology. Whereas the total mean sequencing error rate of yam chlorotic necrosis virus-related MinION reads was 11.25%, we show that the consensus sequence obtained either by de novo assembly or after mapping the MinION reads on the virus genomic sequence was >99.8% identical with the Sanger-derived reference sequence. From the perspective of potential plant disease diagnostic applications of MinION sequencing, these degrees of sequencing accuracy demonstrate that the MinION approach can be used to both reliably detect and accurately sequence nearly full-length positive-sense single-strand polyadenylated RNA plant virus genomes.
dc.language.isoen
dc.publisherNature Publishing Group
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.title.enNanopore-based detection and characterization of yam viruses.
dc.typeArticle de revue
dc.identifier.doi10.1038/s41598-018-36042-7
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
dc.subject.halSciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie
bordeaux.journalScientific Reports
bordeaux.page17879
bordeaux.volume8
bordeaux.issue1
bordeaux.peerReviewedoui
hal.identifierhal-02626561
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02626561v1
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