A global analysis of the Rubus virome using public transcriptome data

Abstract Viruses are the causal agent of some of the most limiting diseases in Rubus crops. In this regard, a detailed knowledge of the Rubus virome is essential for the successful implementation of mitigation strategies and to assess the risk of emergence of novel viral diseases. Fortunately, the widespread use of RNA sequencing to characterize diverse aspects about the biology of Rubus species can also be a valuable source of data on viruses associated with these hosts. Here, we present a meta-analysis of the Rubus virome based on the re-examination of public RNAseq data from nine Rubus species and 23 hybrid cultivars across the world. As a result, we identified 23 viruses and one viroid associated with the genus Rubus. Detected viruses are part of eleven families and 26 genera. We a provide evidence for existence of a second species in the genus Brambyvirus, and a novel member of the family Virgaviridae. Our data also revealed raspberry bushy dwarf virus (RBDV) to be the most prevalent and generalist Rubus virus across the world. In terms of number of species, the genus Ilarvirus and the family Closteroviridae were the most diverse taxonomic rank affecting Rubus. Network analysis revealed distinct Rubus viromes in different countries and analysis of coinfections revealed three main viral communities infecting these plant species across the world. We also provide information on virus variants from new locations across the world and data on potential emergent viruses from other plant hosts.