Pepino mosaic virus: Recombination, spatiotemporal divergence and codon usage

Abstract Pepino mosaic virus (PepMV, species Potexvirus pepini ) is a potexvirus of economic significance. The pathogen has become a serious threat to tomato ( Solanum lycopersicum ) worldwide. To gain more insights into the molecular epidemiology and evolution of PepMV, recombination analysis was carried out. Nine chimeric sequences were identified, including one probably involving host‐to‐virus gene flow. Based on the coat protein ( CP ) gene, PepMV isolates were classified into six genotypes and the phylogeography was reconstructed. Bayesian coalescent analysis applied to the dated genomic sequences suggested that PepMV started to expand in the early 17th century and evolved at a moderate rate. Ancestral state reconstruction supported the South American origin of PepMV. Codon usage bias analysis showed that PepMV genes had influences in addition to compositional constraints. In codon usage, PepMV is fairly similar to S . lycopersicum . Moreover, PepMV recapitulates the host's remarkable suppression of CpG and UpA dinucleotides.