Nucleotide sequences of apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex- and carlaviruses.

The nucleotide sequence (9306 nucleotides) of cDNA clones of apple stem pitting virus (ASPV) obtained from a double-stranded RNA template, extracted from diseased plant tissue, was determined. The genome is composed of five open reading frames (ORFs) encoding putative proteins with M(r)s of 247083, 25147, 12832, 7429 and 43712, and has a poly(A) tail. Using two oligonucleotides designed from the ASPV sequence information a 1598 bp fragment from near the 3' terminus of the viral RNA, containing the coat protein of M(r) 43,766, was amplified from vein yellows (VY)-infected pear plants by PCR. The sequence determined showed eight nucleotide changes resulting in five amino acid substitutions compared with the sequence of ASPV. When compared to potex-, carla-, clostero- and capilloviruses, the ASPV genome organization appeared to be most closely related to that of potexviruses, but with a larger coat protein of M(r) 44K (ORF5). The predicted coat protein size was confirmed by immunoblot analysis. The results show that ASPV does not fall into subgroup A of the closteroviruses but that it probably belongs in an as yet undefined group of viruses. They also suggest that the virus associated with VY is a strain of ASPV.