Sequence analysis of the 3'-terminal halves of RNA 1 of two strains of barley mild mosaic virus

Abstract

DNA complementary to the 3'-terminal halves of RNA 1 of two strains of barley mild mosaic virus (BaMMV) from Japan, BaMMV-Ka1 and BaMMV-Na1, was cloned and sequenced. The sequences start within a single long open reading frame (ORF), and are followed by 337 and 338 3' non-coding nucleotides, for BaMMV-Ka1 and BaMMV-Na1 respectively. The two strains have 88% nucleotide identity in the ORFs and 92% identity in the non-coding regions. The putative ORF products contain the capsid proteins at the C termini, as indicated by amino acid sequence analysis, and two putative non-structural proteins are arranged in the same manner as in RNA 1 of barley yellow mosaic virus (BaYMV). The deduced capsid proteins of BaMMV-Ka1 and BaMMV-Na1 each contain 251 amino acids and have 94% sequence identity, which is compatible with their close serological relationship. Most of the sequence differences between the two capsid proteins are found in the N-terminal region, and might explain their serological differences. Significant sequence similarities of the capsid proteins of the two BaMMV strains (37 and 35% respectively) with that of BaYMV, and their marginal similarities (21 to 26%) to the capsid proteins of aphid-borne or mite-borne potyviruses support the classification of BaMMV and BaYMV as distinct members of the same virus group, which is separate from the group(s) containing aphidborne or mite-borne potyviruses.