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

RNASeq 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 furt...

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Bibliographic Details
Published in:PloS one 2018-10, Vol.13 (10), p.e0206010-e0206010
Main Authors: Nourinejhad Zarghani, Shaheen, Hily, Jean Michel, Glasa, Miroslav, Marais, Armelle, Wetzel, Thierry, Faure, Chantal, Vigne, Emmanuelle, Velt, Amandine, Lemaire, Olivier, Boursiquot, Jean Michel, Okic, Arnela, Ruiz-Garcia, Ana Belén, Olmos, Antonio, Lacombe, Thierry, Candresse, Thierry
Format: Article
Language:English
Subjects:
Agricultural sciences
Biodiversity
Bioinformatics
Biology and Life Sciences
Computer and Information Sciences
Double-stranded RNA
Gene expression
Gene sequencing
Genetic aspects
Genetic diversity
Genomes
Genomic analysis
Life Sciences
Nucleotide sequence
Phylogenetics
Phylogeny
Polymorphism
Proteins
Recombination
Reconstruction
Research and Analysis Methods
Ribonucleic acid
RNA
RNA sequencing
RNA viruses
Stem pitting
Virology
Viruses
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Summary:RNASeq 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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0206010