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
Affiliations
Michael Louie R. Urzo
Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
Timothy D. Guinto
Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
Ana Eusebio-Cope
Fit-for-Future Genetic Resources Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
Bernard O. Budot
Institute of Weed Science, Entomology, and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
Mary Jeanie T. Yanoria
Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
Gilda B. Jonson
Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
Masao Arakawa
Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
Hideki Kondo
Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
Nobuhiro Suzuki
Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
Rice sheath blight, caused by the soil-borne fungus Rhizoctonia solani (teleomorph: Thanatephorus cucumeris, 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 R. solani 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 R. solani populations. Using next-generation sequencing, the viral sequences of the three representative R. solani 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 Martellivirales, Hepelivirales, Durnavirales, Cryppavirales, Ourlivirales, and Ghabrivirales based on their coding-complete RNA-dependent RNA polymerase sequences. The complete genome sequences of two novel RNA viruses belonging to the proposed family Phlegiviridae and family Mitoviridae were determined.
