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

July 2011 , Volume 101 , Number  7
Pages  778 - 785

Alexander V. Karasev, Xiaojun Hu, Celeste J. Brown, Camille Kerlan, Olga V. Nikolaeva, James M. Crosslin, and Stewart M. Gray

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.

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Accepted for publication 7 February 2011.

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 1F5). To characterize this new PVYO-O5 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 PVYO 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.

© 2011 The American Phytopathological Society