Characterization of endogenous Rubus yellow net virus in raspberries

Abstract Rubus yellow net virus (RYNV) belongs to genus Badnavirus. Badnavirids are found in plants as endogenous, inactive sequences, and/or in episomal (infectious and active) forms. To assess the state of RYNV infections, we sequenced the genomes of various Rubus cultivars and mined eight additional published whole genome sequencing datasets. Sequence analysis revealed the presence of a diverse array of endogenous RYNV (endoRYNV) sequences that differ significantly in their structure; some lineages have nearly complete, yet non-functional genomes whereas others have rudimentary, small sequence fragments. We developed assays to genotype the six main endoRYNV lineages as well as the only known episomal lineage in commercial Rubus. This study discloses the widespread presence of endoRYNVs in commercial raspberries, likely because breeding programs have been using a limited pool of germplasm that harbored endoRYNVs.