In recent years, three major fungal diseases of rice, i.e., rice blast, rice false smut, and rice-sheath blight, have caused serious worldwide rice-yield reductions and are threatening global food security. Mycoviruses are ubiquitous in almost all major groups of filamentous fungi, oomycetes, and yeasts. To reveal the mycoviral diversity in three major fungal pathogens of rice, we performed a metatranscriptomic analysis of 343 strains, representing the three major fungal pathogens of rice, Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, sampled in southern China. The analysis identified 682 contigs representing the partial or complete genomes of 68 mycoviruses, with 42 described for the first time. These mycoviruses showed affinity with eight distinct lineages: Botourmiaviridae, Partitiviridae, Totiviridae, Chrysoviridae, Hypoviridae, Mitoviridae, Narnaviridae, and Polymycoviridae. More than half (36/68, 52.9%) of the viral sequences were predicted to be members of the families Narnaviridae and Botourmiaviridae. The members of the family Polymycoviridae were also identified for the first time in the three major fungal pathogens of rice. These findings are of great significance for understanding the diversity, origin, and evolution of, as well as the relationship between, genome structures and functions of mycoviruses in three major fungal pathogens of rice.

Mycovirus is a kind of virus that infects fungi and oomycetes and can replicate in them, which widespread in all major groups of plant-pathogenic fungi and oomycetes. To date, no positive-sense single-stranded RNA (+ ssRNA) virus has been reported to be associated with Ustilaginoidea virens, the notorious causal agent of rice false smut (RFS). Here, we report the molecular characterization of a novel + ssRNA mycovirus, Ustilaginoidea virens narnavirus 1 (UvNV1), isolated from U. virens strain Uv418. UvNV1 has a genome of 3,131 nt and possesses an open reading frame (ORF) predicted to encode an RNA-dependent RNA polymerase (RdRP) of 1,017 amino acids (aa) with a molecular mass of 116.6 kDa. BLASTp analysis revealed that the RdRP showed 50.34% aa similarity to that of the previously described Zhangzhou Narna tick virus 1. Phylogenetic analyses indicated that UvNV1 is highly similar to viruses taxonomically classified in the genus Narnavirus, family Narnaviridae. Taken together, these results clearly demonstrate that UvNV1 is the first + ssRNA virus known to infect U. virens.