Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae. More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts.

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Published in Journal of Virology, v. 90, no. 15, p. 6846-6863.

Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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This work, including the efforts of Shin-Yi Lee Marzano, Berlin Nelson, Glen Hartman, Darin M. Eastburn, and Leslie L. Domier, was funded by National Sclerotinia Initiative. This work, including the efforts of Glen Hartman and Leslie L. Domier, was funded by United States Department of Agriculture.

Related Content

Supplemental material for this article may be found at http://dx.doi.org/10.1128 /JVI.00357-16.

zjv999181807sd1.xlsx (14 kB)
Supplemental Material: Table S1 (Numbers of sequence reads that aligned to each virus genome.)

zjv999181807sd2.xlsx (14 kB)
Supplemental Material: Table S2 (Origins of fungal isolates infected with identified viruses.)