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New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing.

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMARAIS, Armelle
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFAURE, Chantal
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
dc.date.issued2016
dc.identifier.issn1932-6203
dc.description.abstractEnDouble stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3' non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3' NCR were identified in a single Prunus source, with 3' NCRs of 214-312 nt, a size similar to that observed in other foveaviruses, but 567-850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.
dc.language.isoen
dc.publisherPublic Library of Science
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.title.enNew Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing.
dc.typeArticle de revue
dc.identifier.doi10.1371/journal.pone.0146420
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalPLoS ONE
bordeaux.pagee0146420
bordeaux.volume11
bordeaux.issue1
bordeaux.peerReviewedoui
hal.identifierhal-02635462
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02635462v1
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