Nucleotide sequence and evolutionary relationships of cucumber mosaic virus (CMV) strains: CMV RNA 2.

The nucleotide sequence of RNA2 of the Fny strain (subgroup 1) of cucumber mosaic virus (CMV) was determined and compared at both the nucleic acid and protein level with the previously determined corresponding sequence of RNA 2 of the Q strain (subgroup 2) of CMV. Fny -CMV RNA II 2 consisted of 3050 nucleotides and contained a single open reading frame (ORF) of 2571 nucleotides, whereas Q-CMV RNA 2 consists of 3035 nucleotides and contains a single ORF of 2517 nucleotides. At the nucleotide level, there was 71% sequence homology between the two RNAs, while at the protein level sequence homology was 73%. Protein homology was greater (89%) in the central third than in either the N-terminal (64%) or the C-terminal (56%) thirds. The secondary structures of the 3' end of the RNAs were very similar, even though the nucleotide sequence homology between the 3'-terminal 180 nucleotides was only 62%. By contrast, there was 80% sequence homology between the 5'-terminal 86 residue, non-translated regions of the two RNAs. The evolutionary relationships and the divergence and retention of specific sequences among the two CMV strains and other plant viruses are discussed.