Nucleotide sequence of barley yellow mosaic virus RNA 2

The sequence of the 3585 nucleotides [excluding the 3' poly(A) tail] of barley yellow mosaic virus (BaYMV) RNA 2 was obtained by analysis of cDNA clones and by direct RNA sequencing. The first initiation codon at nucleotide 155 was followed by a single long open reading frame encoding a protein of 890 amino acids with an Mr of 98,458. Amino acid sequence comparisons indicated that the BaYMV 98K protein contains a region similar to the C-terminal proteinase domain of the potyvirus helper component (HC) protein towards its N terminus, but that it has no sequences that resemble the N-terminal part of the HC protein or other proteins of potyviruses. The data reveal striking differences in genetic organization between BaYMV RNA 2 and the 5'-terminal region of the potyvirus genome, despite a close genetic relationship between BaYMV RNA 1 and the rest of the potyvirus genome.