Genetic Diversity of the Ordinary Strain of Potato virus Y (PVY) and Origin of Recombinant PVY Strains

Karasev, A. V., Hu, X., Brown, C. J., Kerlan, C., Nikolaeva, O. V., Crosslin, J. M., and Gray, S. M. 2011. Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains. Phytopathology 101:778-785. The ordinary strain of Potato virus Y (PVY), PVYO, causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny gene. A novel substrain of PVYO was recently reported. PVYO-O5, which is spreading in the United States and is distinguished from other PVYO isolates serologically (i.e., reacting to the otherwise PVYN-specific monoclonal antibody IFS). To characterize this new PVYO-05 subgroup and address possible reasons for its continued spread, we conducted a molecular study of PVYO and PVYO-O5 isolates from a North American collection of PVY through whole-genome sequencing and phylogenetic analysis. In all, 44 PVYO isolates were sequenced, including 31 from the previously defined PVYO-O5 group, and subjected to whole-genome analysis. PVYO-O5 isolates formed a separate lineage within the PVYO genome cluster in the whole-genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. On the other hand, the PVYO sequences separated into at least two distinct lineages on the whole-genome phylogenetic tree. To shed light on the origin of the three most common PVY recombinants, a more detailed phylogenetic analysis of a sequence fragment, nucleotides 2,406 to 5,821, that is present in all recombinant and nonrecombinant PVYO genomes was conducted. The analysis revealed that PVYN:O and PVYN-wi recombinants acquired their PVYO segments from two separate PVYO lineages, whereas the PVYNTN recombinant acquired its PVY segment from the same lineage as PVYN:O. These data suggest that PVYN:O and PVYN-wi recombinants originated from two separate recombination events involving two different PVYO parental genomes, whereas the PVYNTN recombinants likely originated from the PVYN:O genome via additional recombination events.