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

First, second, fourth, and fifth authors: Department of PSES, University of Idaho, Moscow, ID 83843; first, second, and third authors: Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID; sixth author: United States Department of Agriculture–Agricultural Research Service (USDA-ARS), Prosser, WA 99350; and seventh author: USDA-ARS, Cornell University, Ithaca, NY 14853.

The ordinary strain of Potato virus Y (PVY), PVY^O, causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny gene. A novel substrain of PVY^O was recently reported, PVY^O-O5, which is spreading in the United States and is distinguished from other PVY^O isolates serologically (i.e., reacting to the otherwise PVY^N-specific monoclonal antibody 1F5). To characterize this new PVY^O-O5 subgroup and address possible reasons for its continued spread, we conducted a molecular study of PVY^O and PVY^O-O5 isolates from a North American collection of PVY through whole-genome sequencing and phylogenetic analysis. In all, 44 PVY^O isolates were sequenced, including 31 from the previously defined PVY^O-O5 group, and subjected to whole-genome analysis. PVY^O-O5 isolates formed a separate lineage within the PVY^O genome cluster in the whole-genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. On the other hand, the PVY^O 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 PVY^O genomes was conducted. The analysis revealed that PVY^N:O and PVY^N-Wi recombinants acquired their PVY^O segments from two separate PVY^O lineages, whereas the PVY^NTN recombinant acquired its PVY^O segment from the same lineage as PVY^N:O. These data suggest that PVY^N:O and PVY^N-Wi recombinants originated from two separate recombination events involving two different PVY^O parental genomes, whereas the PVY^NTN recombinants likely originated from the PVY^N:O genome via additional recombination events.