Genome Reconstruction of Grapevine Virus M and In Silico miRNA Prediction for Sequence-Specific Gene Silencing.

Grapevine is a woody perennial plant susceptible to various viral infections and is propagated mainly on Dogridge rootstock. In this study, ~ 58 million high-quality RNA-seq reads from this grapevine rootstock from a nursery were reassembled into contigs. A contig of 7460 nt displayed 89.23% identity with grapevine virus M (GVM) and was found to be closely related to the sole GVM isolate from the USA (MK492703) while African isolates of GVM grouped separately. RT-PCR and sanger sequencing of coat protein confirmed the presence of GVM in HTS and its three individual sample of rootstocks including 14 out of 19 scion samples. This is the first complete genome study of GVM infecting a rootstock. In order to understand the defense responses to GVM in silico analyses were conducted. In silico analyses identified target binding sites for mature grapevine-derived vvi-miRNAs within the GVM genome. Among them, vvi-miR3632-5p was found as a potential agent for modulating virus infection. The grapevine-derived vvi-miRNAs identified in this study will be helpful in understanding defence strategy during virus host interaction. The impact of GVM on different scion varieties of grapevine requires further investigation.