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

Shaheen Nourinejhad Zarghani (1, 2) , Jean-Michel Hily (3) , Miroslav Glasa (4) , Armelle Marais (5) , Thierry Wetzel (1) , Chantal Faure (5) , Emmanuelle Vigne (3) , Amandine Velt (3) , Olivier Lemaire (3) , Jean-Michel Boursiquot (6) , Arnela Okic (7) , Ana Belén Ruiz-Garcia (8) , Antonio Olmos (8) , Thierry Lacombe (6) , Thierry T. Candresse (5)

1 DLR - Dienstleistungszentren Landlicher Raum Rheinland-Pfalz
2 University of Tehran
3 SVQV - Santé de la vigne et qualité du vin
4 Institute of Virology, Biomedical Research Centre
5 BFP - Biologie du fruit et pathologie
6 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
7 UNSA - University of Sarajevo
8 IVIA - Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research

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.

Domaines: Sciences agricoles

Shaheen Nourinejhad Zarghani, Jean-Michel Hily, Miroslav Glasa, Armelle Marais, Thierry Wetzel, et al.. Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data. PLoS ONE, 2018, 13 (10), 17 p. ⟨10.1371/journal.pone.0206010⟩. ⟨hal-02628866⟩