The Genetic Structure of Populations of Potato virus Y in Japan; Based on the Analysis of 20 Full Genomic Sequences

The genetic structure of Potato virus Y (PVY) populations in Japan was analysed using 20 isolates; five were retrieved from the public DNA sequence databases, and an additional 15 complete genomic sequences were determined using field samples collected in Japan. Recombination and phylogenetic analyses of a total of 149 isolates from Japan and other countries showed that PVY has three major lineages (C, N and O); at least one, two and six sublineages in C, N and O lineages, respectively. One recombination pattern was newly found among Japanese PVYNTN strain isolates, which was most closely related to the PVYNTN strain isolates previously found in Europe and North America. On the other hand, PVYO was a complex of several divergent lineages, and there were at least three non-recombinant subpopulations in Japan. Studies on nucleotide diversities of populations and phylogenetic relationships of the isolates in the PVY sequences showed that Japanese PVY populations were in part distinct from the European and North American populations.