Abstract
Potato virus A (PVA), a member of the genus Potyvirus, is an important potato pathogen that causes 30%–40% yield reduction to global potato production. Knowledge on the genetic structure and the evolutionary forces shaping the structure of this pathogen is limited but vital in developing effective management strategies. In this study, we investigated the population structure and molecular evolution of PVA by analyzing novel complete genomic sequences from Chinese isolates combined with available sequences from Europe, South America, Oceania, and North America. High nucleotide diversity was discovered among the populations studied. Pairwise FST values between geographical populations of PVA ranged from 0.22 to 0.46, indicating a significant spatial structure for this pathogen. Although purifying selection was detected at the majority of polymorphic sites, significant positive selection was identified in the P1, NIa, and NIb proteins, pointing to adaptive evolution of PVA. Further phylogeny–trait association analysis showed that the clustering of PVA isolates was significantly correlated with geographic regions, suggesting that geography-driven adaptation may be an important determinant of PVA diversification.
Highlights
Potato (Solanum tuberosum L.) is the fourth largest staple crop after rice, wheat, and maize, both worldwide and in China (Qu et al, 2005)
After trimming the ambiguously regions from the alignment, we found that all mutations in the Potato virus A (PVA) genome are substations, with two sequences as exceptions, which had one and two codon deletions, respectively
The 66 PVA isolates in this study were composed of 66 haplotypes with an overall haplotype diversity of 1.00 and nucleotide diversity of 0.077 (Table 1)
Summary
Potato (Solanum tuberosum L.) is the fourth largest staple crop after rice, wheat, and maize, both worldwide and in China (Qu et al, 2005). As a vegetatively propagated crop, potato is prone to infection by more than 50 viruses (Valkonen, 2007; Lesley and Michael, 2020). Among these viruses, six have been recognized as major potato viruses: potato leafroll virus, potato virus Y (PVY), potato virus A (PVA), potato virus M, potato virus X (PVX), and potato virus S (Bai et al, 2007; Zhang et al, 2010; Duan et al, 2018; Mao et al, 2019). Potato virus A (PVA) has a narrow host range, mainly infecting the members of Solanaceae (Thomas and Nicotiana, 2004). The yield loss associated with single PVA infections is moderate, it can reach 40% in rare cases
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