Phylogeography and molecular evolution of potato virus Y.

José M Cuevas,Johan C Visser,Santiago F Elena,Emmanuel Jacquot,Dirk U Bellstedt,Agnès Delaunay,Darren P Martin

doi:10.1371/journal.pone.0037853

Abstract

Potato virus Y (PVY) is an important plant pathogen, whose host range includes economically important crops such as potato, tobacco, tomato, and pepper. PVY presents three main strains (PVYO, PVYN and PVYC) and several recombinant forms. PVY has a worldwide distribution, yet the mechanisms that promote and maintain its population structure and genetic diversity are still unclear. In this study, we used a pool of 77 complete PVY genomes from isolates collected worldwide. After removing the effect of recombination in our data set, we used Bayesian techniques to study the influence of geography and host species in both PVY population structure and dynamics. We have also performed selection and covariation analyses to identify evolutionarily relevant amino acid residues. Our results show that both geographic and host-driven adaptations explain PVY diversification. Furthermore, purifying selection is the main force driving PVY evolution, although some indications of positive selection accounted for the diversification of the different strains. Interestingly, the analysis of P3N-PIPO, a recently described gene in potyviruses, seems to show a variable length among the isolates analyzed, and this variability is explained, in part, by host-driven adaptation.

Highlights

RNA viruses are characterized by large population sizes, fast replication and high mutation rates, which results on a huge evolutionary potential [1]
Potato virus Y (PVY) is typemember of the genus Potyvirus in the family Potyviridae [7] and is probably the most widespread virus infecting potatoes, as well as other crops, such as tobacco, tomato and pepper. It was originally classified into strain groups (e.g., PVYC, PVYO and PVYN) according to biological properties or genome sequences [8,9]
Recombination has been commonly described in PVY genomes, where some genomes of recently described isolates are mosaics from previously described PVY genomes [11,12,14,15]

Summary

Introduction

RNA viruses are characterized by large population sizes, fast replication and high mutation rates, which results on a huge evolutionary potential [1]. Two types of genetic exchange, i.e., reassortment in multipartite viruses, and recombination in either segmented or unsegmented viruses, may significantly contribute to speed up adaptation [2]. PVY consists of a single-stranded positive sense RNA genome of about 10000 bases in length [5]. PVY is typemember of the genus Potyvirus in the family Potyviridae [7] and is probably the most widespread virus infecting potatoes, as well as other crops, such as tobacco, tomato and pepper. It was originally classified into strain groups (e.g., PVYC, PVYO and PVYN) according to biological properties or genome sequences [8,9].

Methods

Results

Conclusion