Extreme diversity of mycoviruses present in four strains of Rhizoctonia cerealis, the pathogen of wheat sharp eyespot

Rhizoctonia cerealis is the pathogen of wheat sharp eyespot, which occurs throughout temperate wheat growing regions of the world. In this project, the genomes of viruses from four strains of R. cerealis were analyzed based on Illumina high-throughput RNA-Seq data. Ribosomal RNA-depleted total RNA and purified dsRNA from cultivated mycelia of each isolate were used for cDNA library construction and sequencing. After filtering out reads that mapped to the fungal genome, viral genomes were assembled using the remaining reads from the rRNA-depleted and dsRNA-Seq data. In total, 131 viral genome sequences containing complete ORFs, belonging to 117 viruses, were obtained. Based on phylogenetic analysis, some of them were identified as novel members of the families Curvulaviridae, Endornaviridae, Hypoviridae, Mitoviridae, Mymonaviridae and Phenuiviridae, while others were unclassified viruses. We compared the integrity and reliability of the viral sequences obtained by the two sequencing methods and, for the first time, estimated the density of some viruses in host cells. Most of these viruses from R. cerealis were sufficiently different from those deposited in databases. We propose the establishment of a new family, Rhizoctobunyaviridae, and two new genera, Rhizoctobunyavirus and Iotahypovirus. We further clarified the distribution and co-infection of these viruses in the four R. cerealis strains. In conclusion, the diversity of mycoviruses in R. cerealis is extremely rich. We report a series of novel viruses and provide important insight into virus evolution.