Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada

Summary.

Potato virus Y (PVY) is a serious potato pathogen that affects potato seed and commercial production crops. In recent decades, novel PVY strains have been described that cause necrotic symptoms on tobacco foliage and/or potato tubers. The major PVY strains that affect potato include PVY^O and PVY^N, which have distinct serotypes that can be differentiated by immunoassay. Other economically important strain variants are derived from recombination events, including variants that cause tuber necrotic symptoms (PVY^NTN) and PVY^O serotypes that cause tobacco veinal necrosis (PVY^N-W, PVY^N:O). Although the PVY^NTN and PVY^N-W variants were first reported in Europe, apparently similar strains have been appearing in North America. Confirmation of the existence of these recombinant strains in North America is important, as is whether they spread from a common source or were derived by independent recombination. Whole genome sequencing can be used to positively identify strain variants and begin to address the issue of origins. Symptomology, serology, RT-PCR, and partial sequencing of the coat protein region were used to identify isolates of the PVY^NTN, PVY^N, PVY^NA-N, and PVY^N:O for whole-genome sequencing. Sequencing confirmed the presence of PVY^NTN and PVY^N isolates that were >99% identical to European sequences deposited in GenBank in the 1990’s. Sequences of the PVY^NA-N and PVY^N:O types were 99.0% and 99.5% identical to known sequences, respectively. There was no indication that recombinant strains PVY^NTN or PVY^N:O had different parental origins than recombinant strains previously sequenced. This is the first confirmation by whole-genome sequencing that “European”-type strain variants of PVY^N and PVY^NTN are present in North America, and the first reported full-length sequence of a tuber necrotic isolate of PVY^N:O.