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

Fangluan Gao,Jiasui Zhan,Lianhui Xie,Wenchao Zou

doi:10.1111/eva.12459

Fangluan Gao, Jiasui Zhan + Show 2 more

Open Access

https://doi.org/10.1111/eva.12459

Copy DOI

Abstract

Potato virus Y (PVY) is an important plant pathogen causing considerable economic loss to potato production. Knowledge of the population genetic structure and evolutionary biology of the pathogen, particularly at a transnational scale, is limited but vital in developing sustainable management schemes. In this study, the population genetic structure and molecular evolution of PVY were studied using 127 first protein (P1) and 137 coat protein (CP) sequences generated from isolates collected from potato in China and Japan. High genetic differentiation was found between the populations from the two countries, with higher nucleotide diversity in Japan than China in both genes and a KST value of .216 in the concatenated sequences of the two genes. Sequences from the two countries clustered together according to their geographic origin. Further analyses showed that spatial genetic structure in the PVY populations was likely caused by demographic dynamics of the pathogen and natural selection generated by habitat heterogeneity. Purifying selection was detected at the majority of polymorphic sites although some clade‐specific codons were under positive selection. In past decades, PVY has undergone a population expansion in China, whereas in Japan, the population size of the pathogen has remained relatively constant.

Highlights

Genetic drift, gene flow, and natural selection are three main evolutionary forces shaping the spatial population genetic structure of species (Zhan & McDonald, 2004)
In addition to the high mutation rate in RNA viruses (Domingo, Sheldon, & Perales, 2012), high genetic variation found in both current and previous studies is possibly attributed to the high recombination rate in Potato virus Y (PVY) populations (Gibbs & Ohshima, 2010)
52.69% and 11.76% of concatenated sequences in the Chinese and Japanese populations show a mixed genomic structure of PVYN and PVYO (Table S2). These results re-enforce widespread concern related to the propensity for rapid adaptation of PVY to changing biotic and abiotic environments

Summary

| INTRODUCTION

Gene flow, and natural selection are three main evolutionary forces shaping the spatial population genetic structure of species (Zhan & McDonald, 2004). Knowledge of the population genetics and evolutionary biology of PVY, at a transnational scale, is relatively limited compared to other important plant pathogens such as Magnaporthe (Tredway, Stevenson, & Burpee, 2005), Pyrenophthora (Gurung, Short, & Adhikari, 2013), Verticillium (Short et al, 2015), and Phytophthora (Tian et al, 2016) Many factors such as technology and resource availability may partially contribute to this shortage. With the advance of PCR- based sequencing technology and sharing of sequence data in many public domains, empirical analysis of the population genetic structure and evolutionary biology of biotrophic plant pathogens such as PVY at an international scale has become possible 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. The objectives of this study were to (i) compare the population genetic structure of PVY in China and Japan and (ii) determine the main evolutionary and demographic mechanisms responsible for the observed population genetic structure

| MATERIALS AND METHODS

Findings

| DISCUSSION