The complete nucleotide sequence and genome organization of barley mild mosaic virus (Na1 strain)

The 5'-terminal half of RNA 1 and whole of RNA 2 of barley mild mosaic bymovirus Na1 strain (BaMMV-Na1) were sequenced to give together with the published data its complete genomic sequence. BaMMV-Na1 RNA 1 and RNA 2 consist of 7263 and 3516 nucleotides, excluding the 3' poly A tails, respectively. RNA 1 encodes a single large polyprotein of 2258 amino acids (M(r) 256K), containing eight putative functional proteins, and RNA 2 also encodes one polyprotein of 891 amino acids (M(r) 98K), containing two functional proteins. These functional proteins are arranged in the same manner as in RNA 1 and RNA 2 of barley yellow mosaic bymovirus (BaYMV), and significant amino acid sequence homology (25-58%) exists between the proteins of the two viruses. The BaMMV-Na1 proteins show less amino acid sequence homology (18-32%) with the corresponding proteins of potyviruses or rymoviruses than with those of BaYMV. Comparisons of the BaMMV-Na1 proteins with the corresponding proteins of other partially sequenced BaMMV isolates show 87-98% amino acid sequence identity. There is 91-94% nucleotide sequence identity between the 3' non-coding regions (NCRs) in RNA 1 or RNA 2 of BaMMV-Na1 and other BaMMV isolates, but only 68-72% identity between the 5' NCRs in RNA 2 of BaMMV-Na1 and other BaMMV isolates.