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

Abstract

Diplodia seriata 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 D. seriata. Several viral-like contig sequences were obtained via 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 via 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 Polymycoviridae, Chrysoviridae, Totiviridae and Partitiviridae, and the remaining four identified mycoviruses belong to single-stranded RNA viral families, i.e., Botourmiaviridae, and two previously proposed families “Ambiguiviridae” and “Splipalmiviridae”. 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 Polymycoviridae, “Splipalmiviridae” and “Ambiguiviridae” are involved in the irregular colony phenotype of L3. To our knowledge, this is the first report of diverse virome characterization from D. seriata.

Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids

“…Finally, our study raises important questions regarding the extent of the impact that NCLDV infection of fungi has on productivity and biogeochemical cycling in the marine deep biosphere. Typically, mycoviruses cause persistent infections transmitted intracellularly that do not lyse the host cell [76]. However, not all such infections are asymptomatic.…”

An Overview of Mycoviral Curing Strategies Used in Evaluating Fungal Host Fitness

“…Successful curing has been achieved in numerous studies, few examples include Magnaporthe oryzae [ 61 ], Fusarium nygamai [ 23 , 24 ], Fusarium oxysporum [ 59 ], Aspergillus fumigatus [ 62 ], Trichoderma harzianum [ 63 ], and edible mushrooms [ 64 ]. In some cases, single-spore isolation is reported to be unsuccessful, i.e., Aspergillus niger [ 34 ], Hypomyces chrysospermus [ 65 ], Alternaria alternate [ 57 , 66 – 69 ], and Neofusicoccum parvum [ 70 , 71 ] and in some cases, partial success has been achieved, e.g., Diplodia seriata [ 71 ]. Some fungal strains produce asexual structures such as pycnidia, which yield pycnidiospores (asexual spores).…”

“…Here, we consider the example of Botrytis gemydayirivirus 1 (BGDaV1), whose virions successfully infected the protoplasts of Botrytis cinerea but were lost after the third subculture [ 158 ]. Neofusicoccum parvum victorivirus 3 (NpVV3) virions also successfully infected ∆dcl2 mutant strain of C. parasitica but was lost after repeated subculturing [ 70 , 71 ]. Similar results were observed for Rosellinia necatrix victorivirus 1 (RnVV1) [ 93 ].…”

Discovery of novel RNA viruses through analysis of fungi-associated next-generation sequencing data

“…In recent years, the diversity of known mycoviruses has rapidly increased with the development and widespread application of sequencing technologies [ 16 – 20 ]. According to the classification principles of the International Committee for the Taxonomy of Viruses (ICTV), mycoviruses are currently classified into 24 taxa, consisting of 23 families and 1 genus ( Botybirnavirus ) [ 21 ]. Most mycoviruses belong to double-stranded (ds) RNA viruses, such as families Totiviridae , Partitiviridae , Reoviridae , Chrysoviridae , Megabirnaviridae , Quadriviridae , and genus Botybirnavirus , or positive-sense single-stranded (+ ss) RNA viruses, such as families Alphaflexiviridae , Gammaflexiviridae , Barnaviridae , Hypoviridae , Endornaviridae , Metaviridae and Pseudoviridae .…”