Genetic diversity and evolution of Apple stem pitting virus isolates from pear in China

Abstract

To determine the population structure and mechanisms of molecular evolution of Apple stem pitting virus (ASPV) isolates from pear in China, we compared 48 coat protein (CP) sequences from 31 ASPV pear isolates and 66 Triple Gene Block (TGB) sequences from 44 ASPV pear isolates. Phylogenetic analysis based on these sequences and corresponding sequences from GenBank showed that ASPV grouping in phylogenetic trees was correlated to the host of origin (apple, pear and Korla pear), regardless of gene sequences examined. The ASPV isolates from pear could be divided into six evolutionary divergent subgroups (A–F) based on their CP sequences, and two new subgroups (B and F) were identified in this study. The ASPV isolates could be divided into five evolutionarily divergent groups based on their TGB sequences. Multiple alignment analysis indicated continuous nucleotide insertions or deletions were present in CP of ASPV pear isolates in China. Recombination events were detected in CP and TGB sequences in our study. These results suggest that ASPV CP and TGB genes were under negative selection. Our study suggests that insertion or deletion mutation, selection pressure and recombination play important roles in genetic diversity of ASPV pear isolates in China.