Abstract
Potato virus Y (PVY) is an important plant pathogen infecting solanaceous crops, causing significant losses to global potato and tobacco production. Some aspects of the plant pathology and molecular biology of PVY have been studied intensively, but the evolutionary dynamics of this virus are poorly understood. Here, we performed a comprehensive set of rigorous evolutionary analyses using 177 nucleotide sequences of the viral genome linked protein (VPg) gene, which interacts with the plant eukaryotic translation initiation factor 4E (eIF4E). Our Bayesian analysis reveals that the VPg gene of PVY has been evolving at a rate of 5.60 × 10–4 subs/site/year (95% credibility interval 3.35 × 10–4–8.17 × 10–4), which is equivalent to those of other plant-infecting RNA viruses. We identified different evolutionary constraints on the two clades of PVY, clade N and clade O, whose diverge time were estimated at the year 1861 CE (95% credibility interval 1750–1948 CE). We also found that genetic variations were correlated with geographic regions, suggesting that the evolution of this pathogen is strongly affected by geographical associated factors. Taken together, the results of our study have potential implications for the control strategies of PVY.
Highlights
Potato virus Y (PVY), the type member of the genus Potyvirus (Lefkowitz et al, 2018), is one of the most destructive plant pathogens causing considerable economic losses in Solanaceae crops
All recombination-free viral protein genome-linked (VPg) sequence data from PVY isolates, even those that have combined recombination structure based on whole genome, were used for the subsequent phylogenetic dating and phylodynamic analyses
We found that the index ratios of the observed values to those expected were between 0 and 1 among geographic regions, with association indices of 0.12 (95% credibility interval: 0.07–0.20) and parsimony scores of 0.33 (95% credibility interval: 0.27–0.39), suggesting the evolution of PVY is accounted for a geographic structure but not homogeneous
Summary
Potato virus Y (PVY), the type member of the genus Potyvirus (Lefkowitz et al, 2018), is one of the most destructive plant pathogens causing considerable economic losses in Solanaceae crops. It has become one of the most prevalent viruses of potato and tobacco productions worldwide (Karasev and Gray, 2013; Quenouille et al, 2013). The classic strains (i.e., PVYO and PVYN) are defined according to their reactions in potato cultivars bearing different N genes and in common tobacco (Singh et al, 2008).
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