Population Analysis of Iranian Potato virus Y Isolates Using Complete Genome Sequence

In this study, the full-length nucleotide sequences of four Iranian PVY isolates belonging to PVY(N) strain were determined. The genome of Iranian PVY isolates were 9,703–9,707 nucleotides long encoding all potyviral cistrons including P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP with coding regions of 825, 1,395, 1,095, 156, 1,902, 156, 564, 732, 1,557 and 801 nucleotides in length, respectively. The length of pipo, embedded in the P3 cistron, was 231 nucleotides. Phylogenetic analysis showed that the Iranian isolates clustered with European recombinant NTN isolates in the N lineage. Recombination analysis demonstrated that Iranian PVY(N) isolates had a typical European PVY(NTN) genome having three recombinant junctions while PVY(N) and PVY(O) were identified as the parents. We used dN/dS methods to detect candidate amino acid positions for positive selection in viral proteins. The mean ω ratio differed among different genes. Using model M0, ω values were 0.267 (P1), 0.085 (HC-Pro), 0.153 (P3), 0.050 (CI), 0.078 (VPg), 0.087 (NIa-pro), 0.079 (NIb) and 0.165 (CP). The analysis showed different sites within P1, P3 and CP were under positive selection pressure, however, the sites varied among PVY populations. To the best of our knowledge, our analysis provides the first demonstration of population structure of PVY(N) strain in mid-Eurasia Iran using complete genome sequences and highlights the importance of recombination and selection pressure in the evolution of PVY.