Phylogenetic and population genetic analyses of plantago asiatica mosaic virus isolates reveal intraspecific diversification

Plantago asiatica mosaic virus (PlAMV) infects ornamental lilies and causes severe necrotic symptoms. PlAMV has also been isolated from several perennial weeds, including Plantago asiatica. While multiple isolates from cultivated lilies have been identified and shown to share a high degree of sequence identity with one another, there have been few studies of PlAMV isolates from weeds. Furthermore, a comprehensive phylogenetic analysis of PIAMV isolates from both lilies and weeds has not been performed. Here, we performed phylogenetic and population genetic analyses of the full-length genome sequences of 36 PlAMV isolates, including 14 new isolates obtained in this study. These analyses suggested intraspecific diversification of PlAMV isolates into five clades, including a clade consisting of ornamental lily isolates (Lily clade) and four other clades consisting of isolates from weeds or medicinal plants. The specific clade membership identified by the phylogenetic analysis was mainly correlated with the geographical location of the members of each clade. All PlAMV isolates except those in the Lily clade had a high level of genetic diversity. The Lily clade had a higher level of genetic differentiation from the other clades. The neutrality test suggested that genetic drift contributed to shaping PlAMV isolates in the Lily clade. Infectivity tests with infectious clones of the representative PIAMV isolates to four plant species, including lilies and P. asiatica, showed that isolates in different phylogenetic clades had variation in infectivity to the subset of plant species.