Nanopore Sequencing as a Rapid Tool for the Identification of Cucumber Mosaic Virus Infecting Spearmint (Mentha spicata)

Spearmint (Mentha spicata L.) is one of the most popular mint species in South Korea due to its range of beneficial effects. We collected spearmint plants that exhibited virus-infection-like mosaic and chlorosis foliar symptoms and identified the causal viral pathogen using an Oxford Nanopore Technologies (ONT)-based MinION platform, which is a compact and portable rapid sequencing device. The nearly-complete genomic sequence of the cucumber mosaic virus (CMV) infecting spearmint was determined and consisted of RNA 1 (3120 nt) with ORF1a encoding 991 amino acids, RNA 2 (2968 nt) with ORF2a encoding 857 and ORF2b encoding 111 aa, and RNA 3 (2128 nt) with ORF3a encoding 280 and ORF3b encoding 219 aa. Phylogenetic analysis based on complete coat protein sequences revealed that CMV-CNU-spearmint was a member of the subgroup IA. This is the first report of a natural CMV infection of spearmint in South Korea. The rapid and reliable sequencing tools provided by the ONT can facilitate the surveillance and identification of plant viruses in the field.