The complete nucleotide sequence of Plum pox virus isolates from sweet (PPV-SwC) and sour (PPV-SoC) cherry and their taxonomic relationships within the species.

Abstract

Plum pox virus (PPV) sweet (SwC) and sour (SoC) cherry isolates were the first PPV isolates to be recovered from natural infection in sweet and sour cherry plants, respectively. Their complete nucleotide sequences have been determined finding a deduced genome organisation typical for PPV species. Both genomes are 9795 nucleotides long, excluding the 3' terminal poly(A) tail, and contain an open reading frame of 9432 nt, encoding a polyprotein of 3143 amino acids. The nucleotide and predicted amino acid sequences of PPV-SwC and SoC have been pairwise compared with available sequences of different PPV strains. Although a very high similarity exists between the whole genomes and polyproteins of the two cherry isolates, high levels of divergence have been calculated with sequences of PPV-M, D and EA isolates. In particular, the most considerable divergence has been found in part of 5' non coding region, in regions encoding P1, P3 + 6K1, 6K2 and NIa-VPg proteins as well as in the N-terminal domain of the coat protein. Phylogenetic analysis have been undertaken in order to establish the taxonomic localisation of SwC and SoC isolates within PPV species, showing that they are always clustered together and separated from the rest of PPV strains, being clearly the most distant.