Reprint of “Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes”

Abstract

Mycoviruses can be beneficial to plants in that they can debilitate pathogenic fungi thereby reducing the severity of associated plant diseases. Studies to date have focused primarily on culturable fungi that represent a fraction of natural fungal populations. The nonculturable fungi, however, can harbor diverse populations of mycoviruses that reduce plant disease or enhance resistance to abiotic stress. Metatranscriptome analysis of field-grown plant samples using high-throughput sequencing offers the possibility of unbiased detection and quantification of mycoviruses regardless of the culturability of their fungal hosts together with the complete associated microbial consortia. In this study, we describe the fungal viromes of the phyllosphere of production soybean fields in Illinois, USA by analyzing the metatranscriptomes of thousands of soybean leaf samples collected during the 2008 and 2009 growing seasons. The analyses identified 25 partial genome sequences that represented at least 22 mycovirus genomes, only one of which had been described previously. The novel mycovirus genomes showed similarity to 10 distinct lineages including the genera Alphapartitivirus, Botybirnavirus, Endornavirus, Mitovirus, Mycoflexivirus, Ourmiavirus, Totivirus, Victorivirus, family Tombusviridae, order Mononegavirales, and the recently proposed genus Gemycircularvirus. The present study adds to the wealth of mycoviruses associated with plant phytobiomes and establishes groundwork needed for further characterization of the viruses.

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

“…In silico approaches to mycovirus discovery have become more common ( 15 – 17 ). These approaches search transcriptomic data for sequences similar to RNA-dependent RNA polymerase (RdRp), which is the only conserved gene among RNA viruses and is diagnostic of infection.…”

A novel botybirnavirus with a unique satellite dsRNA causes latent infection in Didymella theifolia isolated from tea plants

“…To date, five botybirnaviruses have been reported in fungi, all infecting filamentous ascomycetes: SsBRV1 and SsBRV2 from S. sclerotiorum ( 20 , 21 ), BpRV1 from B. porri ( 19 ), and ABV1 and AaBbV1 from Alternaria ( 22 , 23 ). Additionally, soybean leaf-associated botybirnavirus 1 (SlaBRVl) was discovered from a metatranscriptomics survey of soybean phyllosphere phytobiomes ( 24 ), while the sequence of Bipolaris maydis botybirnavirus 1 (BmBRV1) from B. maydis has been deposited in NCBI (accession no. MF034086-7).…”

Viruses of endophytic and pathogenic forest fungi

“…Many different approaches have been used to study the biodiversity of mycoviruses, including enrichment of virus-like particles, extraction of dsRNA, and the HTS of small RNA and total RNA [43,76,77]. HTS methods facilitate the rapid discovery of novel viruses by simultaneously generating millions of sequences/reads from hundreds of environmental samples.…”

“…Meta-transcriptomic approaches can also be useful for virus identification [76,78,79]. Notably, Gilbert et al [78] screened transcriptomic data for fungi from the subphylum Pezizomycotina, and found 59 viruses from 44 different fungi based on RNA-seq analyses.…”