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

Abstract

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.

Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection

“…A new degenerate, inosine-containing diagnostic primer was designed to improve the inclusiveness of the detection protocol, which failed to detect these novel isolates. In fact, this kind of primer could help to overcome the high genetic diversity of the virus, even if a lower sensitivity could sometimes result from the degeneracy and inosine contents of the primers [ 9 , 13 , 14 ]. The new primer detected BanMMV infection in two samples that tested negative with the existing primer, but failed to detect three infections among the 110 tested accessions.…”

“…The latter virus displays an important degree of genetic diversity [ 3 , 8 ]. For example, divergent isolates of grapevine virus T, another member of the Betaflexiviridae family, presented nucleotide mismatches at the primer-binding site, which could hamper their detection [ 9 , 10 ]. Therefore, some BanMMV isolates could be missed by very specific diagnostic primers, resulting in false-negative results.…”

A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris)

“…Teroldego, a red Italian grape variety [ 4 ]. Since then, GVT has been reported in different countries, including Germany, France, Croatia, Slovakia, Italy, China and the Czech Republic, where the virus seems to be widespread [ 2 , 7 ]. GRSPaV is another foveavirus infecting grapevine and is nearly ubiquitous among commercially cultivated grapevines worldwide [ 6 ].…”

“…The scale represents 0.1 amino acid substitution per site. The alignment was done on a set including 26 grapevine virus T (GVT) and 21 grapevine rupestris stem pitting-associated virus (GRSPaV) isolates with completely sequenced genomes in order to represent the known diversity of both viruses [ 7 ]. The tree was generated by the maximum-likelihood algorithm with 500 bootstrap replicates using MEGAX.…”

“… The alignment was done on 26 GVT isolates and 21 full-length GRSPaV genome sequences to be representative of the various phylogenetic groups identified for these two grapevine-infecting foveaviruses [ 7 ] …”