Temporal analysis and adaptive evolution of the global population of potato virus M

Abstract Potato virus M (PVM), which is a member of the genus Carlavirus in the family Betaflexviridae , causes critical economic losses of nightshade crops. PVM is transmitted by aphids in a non-persistent manner, by sap inoculation and also transmitted in tubers. Previously, several reports described the genetic structure of PVM. However, the evolutionary rate, timescale, spread and adaptation evolution of the virus have not been examined. In this study, we investigated the phylodynamics of PVM using 145 nucleotide sequences of the coat protein gene and 117 sequences of the cysteine-rich nucleic acid-binding protein (NABP) gene, which were sampled between 1985 and 2013. We found that at least three lineages with isolates that were defined geographically but not by the original host were clustered. The evolutionary rate of the NABP (1.06 × 10 −2 ) was faster than that of the CP (4.12 × 10 −3 ). The time to the most recent common ancestors (TMRCAs) is similar between CP (CIs 31–110) and NABP (CIs 28–33) genes. Based on CP and NABP genes, PVM migrated from China to Canada, Iran, India and European countries, and it circulated within China. Our study is the first attempt to evaluate the evolutionary rates, timescales and migration dynamics of PVM.