Abstract
Over the past five years, research has progressively revealed a rich diversity of RNA viruses in Botrytis cinerea. In this study, we identified nine RNA viruses from the viromes of three B. cinerea strains, including five mitoviruses, one umbra-like virus, and three partitiviruses. Among these, Sclerotinia sclerotiorum partitivirus 1 (SsPV1) was artificially introduced in a previous study. Excluding SsPV1, we cloned the other two partitiviruses and confirmed that both belong to Gammapartitivirus and contain three genomic segments, with dsRNA3 as an RNA satellite. In addition to RNA viruses, we discovered 12 retroplasmids in the three B. cinerea strains. These retroplasmids utilize the mitochondrial genetic codes and only encode a single open reading frame, which is predicted to produce a reverse transcriptase. It is also well known that mitoviruses use the mitochondrial genetic codes to encode their RNA-dependent RNA polymerase. Given the similarities between mitoviruses and retroplasmids in several aspects, we suggest that the mycovirus community could consider whether retroplasmids should be included within the conceptual scope of viruses. Furthermore, this study calls on researchers to pay attention to mobile genetic elements beyond typical RNA viruses, such as the retroplasmids reported here. Additionally, it underscores the importance of using single-spore or single-protoplast isolation methods in mycoviral studies to maintain a consistent genetic and viral background when investigating viral effects on the fungal host.