Population genetics analysis of East Asian Passiflora virus on Amami Oshima Island

Abstract

East Asian Passiflora virus (EAPV) is a member of the genus Potyvirus in the family Potyviridae. In this study, we collected 15 isolates of EAPV from two different areas (the Yuwan area of Uken village and the Sumiyo town of Amami city) on Amami Oshima Island, Japan. The sequences of polyproteins from 10 isolates and the NIb and CP regions of five isolates were determined. The nucleotide and amino acid sequence identities of polyproteins within each population were very high, and those between isolates from both areas were also high. However, five characteristic nonsynonymous substitutions were uniformly observed in the P3 and CP regions of Sumiyo isolates. Recombination analysis revealed that there was no evidence of recombination in any of the isolates from Amami Oshima Island. The selection pressure analysis showed that as a whole, the EAPVs of both populations underwent negative selection but the extent of the negative selection varied. These results were supported by a neutrality test. The gene differentiation and gene flow analysis suggested that the Sumiyo and Yuwan populations were differentiated clearly and gene flow occurred only infrequently. These results were supported by phylogenetic analysis. It was concluded that the two populations evolved independently in each respective area.