Nucleotide sequence and genome organization of a Canadian isolate of the common strain of potato virus Y (PVYO)

The genomic RNA of an isolate (Y-O-139), from field-grown potatoes from Eastern Canada, of the common strain of potato virus Y (PVYO) has been sequenced. The Y-O-139 RNA consists of 9698 nucleotides (nt); therefore it is 5-6 nt shorter than other PVY strains sequenced to date. The first ATG start codon is at nt position 185-187 and the stop codon is at nt 9368-9370, resulting in a putative polyprotein of 3061 amino acids, similar to other PW strains. Comparison of nt sequences of Y-O-139 with partial nt sequence of PVYO isolates from Japan, United Kingdom, and United States shows over 95% homology to several genes. However, only 67, 72, 82, 88, 81, and 91% homology exist with 5'-UTR, P1, HC, NIa-VPg, NIa-Pro, and CP genes, respectively, of a tuber necrotic ringspot strain of PVY (PVYNTN) from Hungary. The Y-O-139 nt sequence shows 97% homology with a PVYN isolate from France (Y-N-F). Comparison of the secondary structures of 5'-UTR and P1 protein coding region of PVYNTN and Y-O-139 showed considerable differences in respective molecules. This is the first report of the complete nucleotide sequence of a commonly occurring PVYO strain.