Evolutionary relationships in the cucumoviruses: nucleotide sequence of tomato aspermy virus RNA 1.

RNA 1 of the V strain of tomato aspermy virus (TAV) consists of 3410 nucleotides and contains one open reading frame (ORF) of 2982 nucleotides, resembling RNA 1 of cucumber mosaic virus (CMV) strains Q and Fny (68% and 66% identical, respectively) and of brome mosaic virus (BMV) (41% identical). In comparisons between amino acid sequences, three conserved regions (N-terminal, C-terminal and central) between TAV and each CMV were found. The N- and C-terminal regions were also conserved with BMV, and contained, respectively, consensus motifs for methyltransferases and for nucleic acid helicases. The 5' and 3' non-coding sequences were highly similar to those of TAV RNA 2. When the sequences for the genomic RNAs of the V and C strains of TAV, and of their encoded products, are compared with those reported for CMV strains representing either subgroup I (Fny-CMV) or subgroup II (Q-CMV) of CMV, it was found that the different virus-encoded proteins are conserved differently between these three viruses. Also, the divergence between TAV and both CMV subgroups has proceeded at different rates for the different ORFs. On the whole, the divergence between TAV and CMV is of the same order as that found between CMV subgroups I and II, which suggests that TAV, Q-CMV and Fny-CMV could be considered as representing three equivalent subgroups of a taxonomic entity.