The Genetic Structure of Populations of Potato virus Y in Japan; Based on the Analysis of 20 Full Genomic Sequences

Abstract

The genetic structure of Potato virus Y (PVY) populations in Japan was analysed using 20 isolates; five were retrieved from the public DNA sequence databases, and an additional 15 complete genomic sequences were determined using field samples collected in Japan. Recombination and phylogenetic analyses of a total of 149 isolates from Japan and other countries showed that PVY has three major lineages (C, N and O); at least one, two and six sublineages in C, N and O lineages, respectively. One recombination pattern was newly found among Japanese PVY NTN strain isolates, which was most closely related to the PVY NTN strain isolates previously found in Europe and North America. On the other hand, PVY O was a complex of several divergent lineages, and there were at least three non-recombinant subpopulations in Japan. Studies on nucleotide diversities of populations and phylogenetic relationships of the isolates in the PVY sequences showed that Japanese PVY populations were in part distinct from the European and North American populations.

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan

“…Consistent with previous results (Ogawa et al., , ; Tian et al., ), high genetic diversities (Table ) were found in both P1 and CP genes in the current study. Each of these two genes encodes a protein with ecological functions that are important to the survival and adaptation of PVY in local biotic and abiotic environments (Quenouille, Vassilakos, & Moury, ).…”

“…This approach has been used by several laboratories to infer the evolution of PVY (Cuevas et al, 2012;Ogawa, Tomitaka, Nakagawa, & Ohshima, 2008), usually involving bona fide geographical populations. Ogawa and colleagues (Ogawa, Nakagawa, Hataya, & Ohshima, 2012;Ogawa et al, 2008) compared the population structure of PVY in Japan, Europe, and North America and found some unique evolutionary patterns associated with the pathogen in Japan. For example, there were only three nonrecombinant subpopulations in Japan (PVY O , PVY N , and PVY NTN ), whereas six subpopulations existed worldwide.…”

Potato virus Y (PVY) in Seed Potato Certification

“…Compared to PVY strain distribution in Germany at the beginning of this century, the shift to recombinant PVY strains has continued. This was observed independently in different geographical regions worldwide (Blanco-Urgoiti et al 1998, Varveri 2006, Lindner 2008, Galvino-Costa et al 2012, Ogawa et al 2012, Upeksha et al 2012, Visser et al 2012, Chikh Ali et al 2013. For example, 87.7% of PVY-infected potato samples analyzed for a census report on PVY in Swiss seed potatoes in 2008 were attributed to recombinants.…”

Occurrence of Potato virus Y strain PVYNTN in foundation seed potatoes in Japan, and screening for symptoms in Japanese potato cultivars

“…Recently, Ogawa et al . () identified three isolates collected from Kyushu and Honshu islands as PVY NTN based on the genomic structure; however, this is the first report of PVY NTN from the Hokkaido region, northern Japan in correlation with the increased PVY infection in foundation seed potatoes in that region.…”