Molecular characterization and complete genome of a putative novel Vigna Yellow Mottle Soymovirus infecting wild red cowpea (Vigna angularis var. nipponensis).

Wild red cowpea (Vigna angularis var. nipponensis) plants exhibiting systemic chlorotic mottles and mosaic patterns on trifoliate leaves were identified during a virus survey in South Korea. High-throughput sequencing of symptomatic leaf samples generated contigs related to members of the genus Soymovirus (family Caulimoviridae). The complete circular double-stranded DNA genome was subsequently determined and validated by PCR amplification and Sanger sequencing. The virus genome is 8,892-nt in length and was tentatively named Vigna yellow mottle soymovirus (VYMSV). Its genomic organization, including primer binding sites, gene arrangement, and open reading frame (ORF) sizes, is largely consistent with those of other soymoviruses, except that ORFI is split into three segments (Ia, Ib, and Ic). The genome contains 10 putative ORFs encoding a movement protein, a coat protein, a replicase polyprotein, a translational activator, and proteins of unknown functions. Pairwise nucleotide sequence comparisons of the reverse transcriptase and RNase H region showed 69.9% identity with Soybean chlorotic mottle virus, consistent with ICTV species demarcation criteria; phylogenetic analysis further corroborated a close evolutionary relationship. Based on these molecular and phylogenetic data, VYMSV represents a putative novel species belonging to the genus Soymovirus. This study expands the known diversity of soymoviruses infecting wild legumes and provides genomic resources for future detection and epidemiological investigations.