Nucleotide Sequence and Evolutionary Relationships of Cucumber Mosaic Virus (CMV) Strains: CMV RNA 2

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Abstract
The nucleotide sequence of RNA 2 of the Fny strain (Subgroup I) 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 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 andd the divergence and retention of specific sequences among the two CMV strains and other plant viruses are discussed.