Diverse spectra of virus infection identified through high throughput sequencing in nursery plants of two Indian grapevine cultivars

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Grapevine (Vitis vinifera L.) is a valuable fruit crop known to be infected by more than 80 viruses and viroidal pathogens globally. In view of absence of indexing system for viruses and lack of information on viruses and viroids in grafted grapevine nursery plants in India, high throughput sequencing (HTS) based virome analysis of four libraries from sample pools and single plants from grafted nursery plants of two commonly grown grapevine cultivars namely Super Sonaka and Anushka was undertaken. RNA sequencing and analysis revealed the infection of 18 viruses and 5 viroids. Grapevine virus A and grapevine virus L (vitiviruses), grapevine leafroll-associated virus-3 (GLRaV-3) and GLRaV-4 (ampeloviruses) were the most predominant in all the grafted nursery plants based on the number of contigs, depth of coverage and copy number. Presence of grapevine virus D, grapevine virus H, and GLRaV-7 have been recorded for the first time in the Indian grapevine. Infection of these viruses obtained in HTS data was confirmed through RT-PCR and sequencing. Using de novo assembly and reference-based mapping, 43 complete or near complete genomes of the identified viruses and viroids were reconstructed from the sequenced grapevine samples. The phylogenetic analysis indicated the possible introduction of identified viruses through the import of infected planting materials which probably escaped quarantine procedure. The study showed the importance of HTS in detection of known and unknown viruses in plant propagules of clonally propagated perennial crops.