Detection and molecular characterization of viruses infecting clematis in Russia

Tomato bushy stunt virus (TBSV), prunus virus I (PrVI), and cucumber mosaic virus (CMV) were found using RT-PCR in the clematis ( Clematis spp.) cultivar collection of the Nikita Botanical Gardens, Yalta, Russia. PrVI was detected in clematis for the first time that extends both the list of viruses infecting this crop and the information on the geographical distribution and host range of PrVI. Using high-throughput sequencing, the nearly complete genomes of TBSV, PrVI, CMV, and clematis chlorotic mottle virus, which was previously found in the collection, were assembled and characterized. The genome of TBSV was most closely related to the cherry strain of this virus sharing 95.9% identity. Five open reading frames of the PrVI isolate from clematis were 95.8 to 97.7% and 95.6 to 98.6% identical to PrVI from sweet cherry at the nucleotide and amino acid levels, respectively. CMV was revealed in a single plant of the introduced cultivar Valge Daam. Based on phylogeny of complete genomes, RNA1, RNA2, and RNA3 identities, and the size of the proteins 2a and 2b (840 and 100 amino acid residues, respectively), the CMV isolate was shown to belong to subgroup II. TBSV, CMV, and PrVI did not induce visible symptoms on leaves or flowers of at least some clematis cultivars. This is the first report about clematis viruses in Russia and the first molecular characterization of TBSV, PrVI, and CMV isolates from clematis.