Novel Mycoviruses Discovered from a Metatranscriptomics Survey of the Phytopathogenic Alternaria Fungus

Abstract

<i>Alternaria</i> fungus can cause notable diseases in cereals, ornamental plants, vegetables, and fruits around the world. To date, an increasing number of mycoviruses have been accurately and successfully identified in this fungus. In this study, we discovered mycoviruses from 78 strains in 6 species of the genus <i>Alternaria</i>, which were collected from 10 pear production areas using high-throughput sequencing technology. Using the total RNA-seq, we detected the RNA-dependent RNA polymerase of 19 potential viruses and the coat protein of two potential viruses. We successfully confirmed these viruses using reverse transcription polymerase chain reaction with RNA as the template. We identified 12 mycoviruses that were positive-sense single-stranded RNA (+ssRNA) viruses, 5 double-strand RNA (dsRNA) viruses, and 4 negative single-stranded RNA (-ssRNA) viruses. In these viruses, five +ssRNA and four -ssRNA viruses were novel mycoviruses classified into diverse the families <i>Botourmiaviridae,&nbsp;Deltaflexivirus, Mymonaviridea, and Discoviridae</i>. We identified a novel -ssRNA mycovirus isolated from an <i>A</i>. <i>tenuissima</i> strain HB-15 as Alternaria tenuissima negative-stranded RNA virus 2 (AtNSRV2). Additionally, we characterized a novel +ssRNA mycovirus isolated from an <i>A</i>. <i>tenuissima</i> strain SC-8 as Alternaria tenuissima deltaflexivirus 1 (AtDFV1). According to phylogenetic and sequence analyses, we determined that AtNSRV2 was related to the viruses of the genus <i>Sclerotimonavirus</i> in the family <i>Mymonaviridae</i>. We also found that AtDFV1 was related to the virus family <i>Deltaflexivirus</i>. This study is the first to use total RNA sequencing to characterize viruses in <i>Alternaria</i> spp. These results expand the number of <i>Alternaria</i> viruses and demonstrate the diversity of these mycoviruses.