RNA-dependent RNA polymerase domain-based molecular characterisation and evolutionary analysis of potato virus S

Abstract

Potato virus S (PVS) is a globally distributed Carlavirus that infects potato (Solanum tuberosum L.) and related Solanum species. While it often causes mild symptoms, it can have a notable impact on crop productivity. This study examined the genetic diversity and phylogenetic structure of PVS isolates from India using complete genome sequences and the RNA-dependent RNA polymerase (RdRP) domain of the replicase gene, with the aim of assessing the suitability of RdRP as a molecular marker for evolutionary inference. A global dataset of 151 PVS sequences was analysed, along with RdRP domain sequences from 11 Indian isolates and complete genome sequences from two representative isolates. Sequence demarcation tool (SDT) analysis showed pairwise nucleotide identities ranging from 73.8–100 % for complete genomes and 82.2–100 % for RdRP domains. Using a 92 % nucleotide identity threshold, the PVS isolates were grouped into eightintraspecific phylogenetic clades (G1–G8). Phylogenetic trees inferred from RdRP domain sequences showed high topological congruence with complete genome phylogenies, as confirmed by tanglegram analysis. In addition, these phylogenetic groups also broadly matched previously reported PVS phylogroups, including the predominant PVS-O lineage. Population genetic analyses indicated stronger host-associated structuring than geographic differentiation, while the RdRP domain exhibited low nucleotide diversity and strong purifying selection. Collectively, these findings indicate that RdRP domain-based analysis provides a reliable and efficient approach for PVS molecular characterisation, comparative evolutionary studies and the identification of divergent or putative novel PVS variants.