Comparative genetic diversity of potato virus Y populations based on coat protein gene

Potato virus Y (PVY) is an important plant pathogen with a wide host range including economically important crops of potato, tobacco, tomato, and pepper. The coat protein gene has been commonly used in studying molecular biology of plant viruses including PVY. In this study, we used a large dataset of CP sequences from isolates collected across the world to assess the detailed molecular evolution of PVY populations with a focus on the Iranian PVY population. Phylogenetic analysis showed that the world PVY population had two major lineages (O:C and N:NTN); each comprising several divergent sublineages. Results showed that the Iranian PVY isolates were distributed across the tree suggesting polyphyletic origin of the Iranian PVY population. Statistical analysis revealed great genetic differences between pairs of the PVY phylogenetic populations. Host populations and also geographical populations of PVY were genetically differentiated. The extent of the genetic diversification among PVY host and geographical populations were mild or moderate. Purifying selection was detected on the CP gene sequences of the PVY populations, suggesting that most of the mutations in the gene were harmful, thereby were eliminated by natural selection. We also detected a variety of recombination patterns to occur along the CP gene of the PVY strains. A significant number of the Iranian PVY isolates were found to be recombinant. Different analyses suggest that Iranian PVY population is highly diverse. In conclusion, results of this study demonstrated that different factors including mutation, host adaptation, geographical distinction and selection pressure shaped the genetic structure of the PVY populations.