Metagenomic analysis of ampelographic collections of Dagestan revealed the presence of two novel grapevine viruses

In this study, we performed an analysis of the viromes of 73 grape samples from two Dagestan ampelographic collections in Russia using the high-throughput sequencing of total RNAs. 14 viruses and 4 viroids were identified, with 1 to 11 of them detected in each plant. For the first time in Russia, we identified Grapevine leafroll associated virus 7 and Grapevine Kizil Sapak virus. 206 genomes of viruses and viroids were obtained and their phylogenetic analysis was carried out. The de novo assembly and tblastx analysis allowed to obtain contigs of a novel (+) ssRNA genome of a plant virus from the genus Umbravirus that was tentatively named Grapevine umbra-like virus (GULV), as well as contigs of a novel dsDNA pararetrovirus from the genus Caulimovirus that was tentatively named Grapevine pararetrovirus (GPRV). Complete genomes of these viruses were obtained and used for Sequence Demarcation Tool (SDT) analysis and phylogeny studies. GULV and GPRV were detected in 16 and 33 germplasm samples from the Dagestan collections, respectively.