Exploring the Virome of Blackberry and Wild Rubus spp. in South Carolina

Numerous viruses infect blackberry, and they are associated with virus disease complexes with complicated etiologies. Blackberry virus diseases limit the lifespan of blackberry production in the Southeastern United States. Although some previous research has been conducted to understand which viruses are prevalent in South Carolina, a comprehensive study on the virome of blackberry has not been done in this region. Additionally, the role of wild Rubus as a virus inoculum source is likely underappreciated and represents a potential opportunity for disease management. We took a comprehensive approach to characterize viral genome sequences from known and novel viruses using metatranscriptomic sequencing of blackberry and wild Rubus spp. leaf samples collected in 2021 from eight sites across South Carolina. We detected 17 known and 6 novel plant viruses and describe relevant genome sequence information. Although the etiologies of these novel viruses are yet to be elucidated, they should be considered part of the blackberry/wild Rubus virome and further studied. We describe instances of potential connectivity of virus populations between cultivated blackberry and wild Rubus for several viruses at several sites. In addition to plant viruses, we describe numerous viruses likely associated with foliar fungi, referred to as Rubus leaf-associated viruses. This study revealed a diverse landscape of both known and novel viruses in blackberry and wild Rubus in South Carolina and has stimulated topics for future research, such as temporal analyses of virus spread at the landscape scale and investigating potential vectors and the biological relevance of novel viruses.