Metatranscriptomic Sequencing of Sheath Blight-Associated Isolates of <i>Rhizoctonia solani</i> Revealed Multi-Infection by Diverse Groups of RNA Viruses
Michael Louie R. Urzo | Timothy D. Guinto | Ana Eusebio-Cope | Bernard O. Budot | Mary Jeanie T. Yanoria | Gilda B. Jonson | Masao Arakawa | Hideki Kondo | Nobuhiro Suzuki
Rice sheath blight, caused by the soil-borne fungus <i>Rhizoctonia solani</i> (teleomorph: <i>Thanatephorus cucumeris,</i> Basidiomycota), is one of the most devastating phytopathogenic fungal diseases and causes yield loss. Here, we report on a very high prevalence (100%) of potential virus-associated double-stranded RNA (dsRNA) elements for a collection of 39 fungal strains of <i>R. solani</i> from the rice sheath blight samples from at least four major rice-growing areas in the Philippines and a reference isolate from the International Rice Research Institute, showing different colony phenotypes. Their dsRNA profiles suggested the presence of multiple viral infections among these Philippine <i>R. solani</i> populations. Using next-generation sequencing, the viral sequences of the three representative <i>R. solani</i> strains (Ilo-Rs-6, Tar-Rs-3, and Tar-Rs-5) from different rice-growing areas revealed the presence of at least 36 viruses or virus-like agents, with the Tar-Rs-3 strain harboring the largest number of viruses (at least 20 in total). These mycoviruses or their candidates are believed to have single-stranded RNA or dsRNA genomes and they belong to or are associated with the orders <i>Martellivirales</i>, <i>Hepelivirales</i>, <i>Durnavirales</i>, <i>Cryppavirales</i>, <i>Ourlivirales</i>, and <i>Ghabrivirales</i> based on their coding-complete RNA-dependent RNA polymerase sequences. The complete genome sequences of two novel RNA viruses belonging to the proposed family <i>Phlegiviridae</i> and family <i>Mitoviridae</i> were determined.
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