Application of next generation sequencing in identification of cowpea viruses

Cowpea (Vigna unguiculata L. Walp) is an important legume particularly in the eastern and northern regions of Uganda. Its production is greatly affected by the occurrence of several diseases caused mainly by viral pathogens. Previous studies employed in the detection of cowpea viruses in the country relied largely on specific methods thus offering a partial description of the disease etiology. In this study, virus symptomatic leaf samples were assayed for the presence of viruses using a high throughput sequencing method. Leaf samples were collected from four agro-ecological zones (AEZs) in Uganda and used for total RNA extraction. From the total RNA, cDNA was synthesized and then sequenced using the Illumina Miseq platform. BLASTN analysis revealed the presence of contig sequences with >80% identity to Cowpea aphid borne mosaic virus (CABMV), Peanut mottle virus (PMV), Crotalaria mosaic virus, South African passiflora and Sesame mosaic virus. Analysis also revealed sequences that showed high similarity to Maize dwarf mosaic virus (MDMV), Sugarcane mosaic virus (SCMV) and Maize chlorotic mottle virus (MCMV). This is the first report of cowpea serving as a legume host for MCMV, SCMV and MDMV and given the increasing legume-cereal intensification in the country, this presents a risk of virus spread to maize.