A V2-SKP1 interface in soybean stay-green associated virus: evidence from evolutionary and structural analyses

Soybean stay-green associated virus (SoSGV) is an emerging begomovirus associated with severe disease in soybean crops in East Asia. This study investigated its evolutionary relationships, population structure, recombination history, adaptive signal, and candidate host-interaction features using integrated phylogenetic, population genetic, natural selection, and structural modeling analyses of 54 complete genome sequences. Maximum-likelihood and Bayesian phylogenetic analyses recovered SoSGV as a distinct monophyletic lineage, with strong support in the maximum-likelihood analysis (96% bootstrap support). Population genetic analysis revealed high haplotype diversity (Hd = 0.962), moderate nucleotide diversity (π = 0.022), and a negative Tajima's D value (D = - 1.49, p < 0.05), a pattern consistent with recent demographic expansion but not, by itself, proof of emergence timing. Recombination screening identified two robust coat protein-associated events (best p = 1.95 × 10⁻⁷ and 1.91 × 10⁻¹⁴), and sliding-window similarity analysis independently supported the resulting mosaic structure. Natural selection analyses detected adaptive signal in the V2 gene; MEME identified episodic selection at residues 35 and 36 (p < 0.1), while complementary methods supported additional method-dependent signals. ColabFold predicted a moderate-confidence V2 structure (mean pLDDT = 73.36). Protein docking identified a plausible V2-SKP1-related interface comprising 39 contacting residues, while a short 10 ns molecular dynamics simulation indicated preliminary structural compatibility rather than biological validation. These findings support the hypothesis that recombination contributed to SoSGV diversification and that V2 may interact with SKP1-related host proteins.