Analysis of the Tomato Aspermy Virus Complete Genomes Suggests Reassortment in Russian Isolates from Chrysanthemum

Tomato aspermy virus (TAV, genus Cucumovirus from the family Bromoviridae) is one of the most common and harmful chrysanthemum viruses, causing severe flower distortion, size reduction and color breaking. Metatranscriptome sequencing of chrysanthemum plants of the Ribonette and Golden Standard cultivars from the collection of the Nikita Botanical Garden (Yalta, Republic of Crimea) generated TAV-related reads. The complete genomes of two Russian isolates of the virus were assembled from the reads obtained. This is the first report of full-length TAV genomes from Russia. Typically of cucumoviruses, the segmented TAV genome is represented by three single-stranded positive-sense linear RNA molecules with a length of 3412 (RNA1), 3097 (RNA2) and 2219 (RNA3) nucleotides. Five open reading frames (ORF) have been identified that encode replicase (ORF1), RNA-dependent RNA polymerase (ORF2a), silencing suppressor protein (OFR2b), movement protein (OFR3a) and the virus coat protein (ORF3b). The identity of the TAV genomes from the two chrysanthemum cultivars was 99.8% for all three viral RNAs, and with other TAV isolates from Genbank – 97.5–99.7 (RNA1), 93.8–99.8 (RNA2), and 89.3–99.3% (RNA3). Phylogenetic analysis showed that RNA1 and RNA3 of the Russian isolates were assigned to heterogeneous groups of TAV isolates found on various plant species in different regions of the world. At the same time, RNA2 clearly clustered with tomato isolates SKO20ST2 from Slovenia and PV-0220 from Bulgaria and, to a lesser extent, with the Iranian isolate Ker.Mah.P from petunia and the Chinese isolate Henan from chrysanthemum. The incongruence of phylogenetic trees reconstructed from different segments of the viral genome suggests pseudo-recombination (reassortment) in the Russian TAV isolates.