title: Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains.
abstract: 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.
authors.affiliation: Department of PSES, University of Idaho, Moscow, ID 83843, USA. akarasev@uidaho.edu
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Karasev
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Hu
authors.forename: Celeste J
authors.initials: CJ
authors.lastname: Brown
authors.forename: Camille
authors.initials: C
authors.lastname: Kerlan
authors.forename: Olga V
authors.initials: OV
authors.lastname: Nikolaeva
authors.forename: James M
authors.initials: JM
authors.lastname: Crosslin
authors.forename: Stewart M
authors.initials: SM
authors.lastname: Gray
mesh_terms: D000595:Amino Acid Sequence; D000911:Antibodies, Monoclonal / Q000276:immunology; D001483:Base Sequence; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics; D027462:Chenopodium / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D018515:Plant Leaves / Q000821:virology; D017800:Potyvirus / Q000145:classification* / Q000235:genetics* / Q000276:immunology / Q000472:pathogenicity; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012703:Serotyping; D011198:Solanum tuberosum / Q000821:virology*; D014026:Nicotiana / Q000821:virology
chemical_list: D000911:Antibodies, Monoclonal; D036022:Capsid Proteins; D012367:RNA, Viral