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Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data

hal.structure.identifierDienstleistungszentren Landlicher Raum Rheinland-Pfalz [DLR]
hal.structure.identifierUniversity of Tehran
dc.contributor.authorNOURINEJHAD ZARGHANI, Shaheen
hal.structure.identifierSanté de la vigne et qualité du vin [SVQV]
dc.contributor.authorHILY, Jean-Michel
hal.structure.identifierInstitute of Virology, Biomedical Research Centre
dc.contributor.authorGLASA, Miroslav
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMARAIS, Armelle
hal.structure.identifierDienstleistungszentren Landlicher Raum Rheinland-Pfalz [DLR]
dc.contributor.authorWETZEL, Thierry
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFAURE, Chantal
hal.structure.identifierSanté de la vigne et qualité du vin [SVQV]
dc.contributor.authorVIGNE, Emmanuelle
hal.structure.identifierSanté de la vigne et qualité du vin [SVQV]
dc.contributor.authorVELT, Amandine
hal.structure.identifierSanté de la vigne et qualité du vin [SVQV]
dc.contributor.authorLEMAIRE, Olivier
hal.structure.identifierAmélioration génétique et adaptation des plantes méditerranéennes et tropicales [UMR AGAP]
dc.contributor.authorBOURSIQUOT, Jean-Michel
hal.structure.identifierUniversity of Sarajevo [UNSA]
dc.contributor.authorOKIC, Arnela
hal.structure.identifierInstituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research [IVIA]
dc.contributor.authorRUIZ-GARCIA, Ana Belén
hal.structure.identifierInstituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research [IVIA]
dc.contributor.authorOLMOS, Antonio
hal.structure.identifierAmélioration génétique et adaptation des plantes méditerranéennes et tropicales [UMR AGAP]
dc.contributor.authorLACOMBE, Thierry
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
dc.date.issued2018
dc.identifier.issn1932-6203
dc.description.abstractEnRNASeq or double-stranded RNA based approaches allowed the reconstruction of a total of 9 full-length or near full-length genomes of the recently discovered grapevine virus T (GVT). In addition, datamining of publicly available grapevine RNASeq transcriptome data allowed the reconstruction of a further 14 GVT genomes from five grapevine sources. Together with four GVT sequences available in Genbank, these novel sequences were used to analyse GVT diversity. GVT shows a very limited amount of indels variation but a high level of nucleotide and aminoacid polymorphism. This level is comparable to that shown in the closely related grapevine rupestris stem pitting-associated virus (GRSPaV). Further analyses showed that GVT mostly evolves under conservative selection pressure and that recombination has contributed to its evolutionary history. Phylogenetic analyses allow to identify at least seven clearly separated groups of GVT isolates. Analysis of the only reported PCR GVT-specific detection primer pair indicates that it is likely to fail to amplify some GVT isolates. Taken together these results point at the distinctiveness of GVT but also at the many points it shares with GRSPaV. They constitute the first pan-genomic analysis of the diversity of this novel virus.
dc.language.isoen
dc.publisherPublic Library of Science
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.title.enGrapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data
dc.typeArticle de revue
dc.identifier.doi10.1371/journal.pone.0206010
dc.subject.halSciences du Vivant [q-bio]/Sciences agricoles
bordeaux.journalPLoS ONE
bordeaux.page17 p.
bordeaux.volume13
bordeaux.issue10
bordeaux.peerReviewedoui
hal.identifierhal-02628866
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02628866v1
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