UC Riverside Undergraduate Research Journal

Plant viruses cause serious disease and losses in domesticated crops. However, we know little about plant viruses outside of agriculture. One reason for this is the lack of symptoms of virus infection in wild plants to promptly diagnose and identify with targeted methods. This is now changing with the availability of untargeted “next-generation” sequencing technologies to analyze the viromes of asymptomatic wild plants and study virus impacts on plant health. In this study, we determined whether key winter-growing perennials in local reserves are infected with crop-associated viruses. A previous study in the same locations found that summer-growing perennials host co-infections by multiple crop-associated viruses, but winter-growing plants have not been explored. To enrich for virus sequences, we extracted doubled-stranded RNA, a unique feature of virus replication. We sequenced this material using the Illumina NextSeq platform, then assembled and identified viruses using Galaxy software. In contrast to summer-growing plants, we detected just one crop-associated virus in winter plants: the generalist, Cucumber mosaic virus (CMV). Phylogenetic analysis shows this CMV is in subgroup IA, the most prevalent in the United States. Our results suggest that winter-growing plant viromes have minimal overlap with summer-growing plant viromes and that winter plants may be less exposed to crop-associated viruses.