Nucleotide sequence of barley yellow mosaic virus RNA 1: a close evolutionary relationship with potyviruses

The complete nucleotide sequence of barley yellow mosaic virus (BaYMV) RNA 1 was obtained by analysis of overlapping cDNA clones and by direct RNA sequencing. The sequence is 7632 nucleotides in length, excluding a 3' poly(A) tail. The first AUG codon at nucleotide 172 appeared to be the initiator for a single long open reading frame encoding a protein of 2410 amino acids with an Mr of 270,755. Amino acid sequence comparisons revealed that the BaYMV 270K protein contains three regions upstream of the C-terminal capsid protein which share significant homologies with the cytoplasmic inclusion and two nuclear inclusion proteins of potyviruses thus indicating their similarities in genetic organization. However, the apparent low levels of homology in the corresponding proteins of BaYMV and potyviruses are in contrast with the high conservation among potyviruses. Moreover, our data indicate that BaYMV RNA 1 has no counterpart to the two cistrons located in the 5'-terminal region of the potyvirus genome. Although the data suggest a close evolutionary relationship between BaYMV and potyviruses, the striking differences set BaYMV apart from potyviruses.