Cloning and sequencing of the 3′ half of a potato virus Y (O strain) genome encoding the 5k protein, protease, polymerase and coat protein

Potato virus Y (PVY) is the type member of the potyvirus group that is the largest of the plant virus groups. Among several PVY strains, PVY° strains are spread worldwide (1) and PVY-O is one of Japanese PVY° strains. We propagated PVY-0 on Nicotiana tabacum cv. Samsun NN and isolated its genomic RNA. The synthesized double-stranded cDNA was inserted into the EcoKl site of pBR322 using £coRI linker after the modification of internal EcoJU sites with EcoRl methylase. A 5.0-kb cDNA was cloned and its nucleotide sequence was determined. A poly(dA) tract was found at one end of the cDNA, implying that the cDNA corresponds to the 3'-half PVY-O genomic RNA. The sequence around the distal EcoHl end does not agree with the linker sequence, suggesting that it is an intrinsic EcoKI site which escaped from the methylation. The region spanning from the 5' end to the 4667th nucleotide of the cDNA, which consists of 4998 nucleotides and the poly(dA) tract, forms a part of a long open reading frame (ORF). Four consensus sequences of the potyviral protease cleavage site, i.e., three pieces of VXXQ/A and one VXXQ/G, were found in the deduced amino acid sequence of the ORF. The structure of C-terminal half of PVY-