Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan

Abstract

<i>Diplodia seriata</i> in the family Botryosphaeriaceae is a cosmopolitan phytopathogenic fungus and is responsible for causing cankers, fruit rot and leaf spots on economically important plants. In this study, we characterized the virome of a single Pakistani strain (L3) of <i>D. seriata</i>. Several viral-like contig sequences were obtained <i>via</i> a previously conducted next-generation sequencing analysis. Multiple infection of the L3 strain by eight RNA mycoviruses was confirmed through RT-PCR using total RNA samples extracted from this strain; the entire genomes were determined <i>via</i> Sanger sequencing of RT-PCR and RACE clones. A BLAST search and phylogenetic analyses indicated that these eight mycoviruses belong to seven different viral families. Four identified mycoviruses belong to double-stranded RNA viral families, including <i>Polymycoviridae</i>, <i>Chrysoviridae</i>, <i>Totiviridae</i> and <i>Partitiviridae</i>, and the remaining four identified mycoviruses belong to single-stranded RNA viral families, i.e., <i>Botourmiaviridae</i>, and two previously proposed families "<i>Ambiguiviridae</i>" and "<i>Splipalmiviridae</i>". Of the eight, five mycoviruses appear to represent new virus species. A morphological comparison of L3 and partially cured strain L3ht1 suggested that one or more of the three viruses belonging to <i>Polymycoviridae</i>, "<i>Splipalmiviridae</i>" and "<i>Ambiguiviridae</i>" are involved in the irregular colony phenotype of L3. To our knowledge, this is the first report of diverse virome characterization from <i>D. seriata</i>.