Full genome sequence of a putative novel mitovirus isolated from Rhizoctonia cerealis

Abstract

A putative novel mitovirus was found in isolate R1084 of the fungus Rhizoctonia cerealis, the causal agent of sharp eyespot of wheat in China. The full genome sequence of the virus was determined and analyzed. The complete cDNA sequence is 3149 nucleotides long with 59.7% A+T content. Using either the fungal mitochondrial or universal genetic code, the viral genome was found to contain a single large open reading frame that is predicted to encode a protein of 812 amino acids with an RNA-dependent RNA polymerase (RdRp) domain that is conserved in the mitovirus RdRp superfamily. The amino acid sequence of the RdRp domain is only 50% identical to the corresponding domain in Sclerotinia sclerotiorum mitovirus 11, and therefore, this virus is proposed to be a novel mitovirus, designated as Rhizoctonia cerealis mitovirus 1-R1084 (RcMV1-R1084). The distinct codon usage of RcMV1-R1084 hints that this virus is potentially able to replicate not only in mitochondria but also in the cytoplasm. This is the first report of a full-length genomic sequence of a putative mitovirus in R. cerealis.

Evidence for contemporary plant mitoviruses

“…We therefore also searched the SRA data sets from these other projects for sequence reads highly similar to those of the original TSA hits from the respective plant species. Having identified such reads from several studies (Table S1), we were then able to assemble them into contigs that appear to represent nearly complete mitovirus genome sequences from three other sugar beet strains of Beta vulgaris (BioProjects PRJNA41497 and PRJNA254489; Dohm et al, 2014; Stracke et al, 2014), three other strains or sources of Cannabis sativa (hemp) (BioProjects PRJNA73819, PRJNA80055, and PRJNA178769; van Bakel et al, 2011), another source of Dahlia pinnata (a common ornamental) (BioProject PRJNA193277; Hodgins et al, 2014), another source of Erigeron breviscapus (a Chinese species of fleabane used in traditional medicine) (BioProjects PRJNA229196 and PRJNA277583; Zhang et al, 2015), and another source of Petunia exserta (a Brazilian species of increasing use as an ornamental) (BioProject PRJNA300556; Sheehan et al, 2016) (Table 1; other assembly details in Table S2).…”

“…In current, ICTV-ratified taxonomy, family Narnaviridae comprises two genera, Narnavirus and Mitovirus , respectively containing two and five species of fungal viruses: Saccharomyces 20S RNA narnavirus and Saccharomyces 23S RNA narnavirus in genus Narnavirus ; Cryphonectria mitovirus 1 , Ophiostoma mitovirus 3a , Ophiostoma mitovirus 4 , Ophiostoma mitovirus 5 , and Ophiostoma mitovirus 6 in genus Mitovirus (Buck et al, 2005; Hong et al, 1998, 1999; Polashock and Hillman, 1994). Despite this small representation, many other apparent Mitovirus members have been reported to date from fungal hosts (Abdoulaye et al, 2017; Bartholomäus et al, 2016; Das et al, 2016; Heinze, 2012; Hillman and Cai, 2013; Khalifa and Pearson, 2014; Kitahara et al, 2014; Lakshman et al, 1998; Marzano et al, 2016; Vainio et al, 2015; Xie and Ghabrial, 2013; Xu et al, 2015; Zhang et al, 2015). Indeed, more than 90 accessions in the Nucleotide (nr/nt) database at GenBank appear to encompass the complete coding sequences of additional fungal mitoviruses.…”

Mitovirus UGA(Trp) codon usage parallels that of host mitochondria

“…In particular, two viruses from Rhizophagus species (phylum Mucoromycota, subphylum Glomeromycotina) (Kitahara et al, 2014), ten viruses from Rhizoctonia species (phylum Basidiomycota, subphylum Agaricomycotina) (Abdoulaye et al, 2017; Bartholomäus et al, 2016; Das et al, 2016; Lakshman et al, 1998; Marzano et al, 2016; Zhang et al, 2015), and one virus from Macrophomina phaseolina (phylum Ascomycota, subphylum Pezizomycotina) (Marzano et al, 2016) contain no UGA codons. Additionally, three other viruses from Rhizoctonia solani (Marzano et al, 2016) and one each from Agaricus bisporus and Clitocybe odora (phylum Basidiomycota, subphylum Agaricomycotina) (Heinze, 2012) contain only a low percentage of UGA codons (4–21%) vs. UGG codons (79–96%).…”

“…Several previous authors have noted that any such mitoviruses with no UGA codons might express their RdRps and replicate their genomes not only in mitochondria but also or instead in the cytosol of their respective hosts (Das et al, 2016; Hillman and Cai, 2013; Hong et al, 1999; Kitahara et al, 2014; Lakshman et al, 1998; Zhang et al, 2015). Moreover, such capacity for cytosolic replication might have provided the selective pressure for this subset of mitoviruses to lack UGA codons.…”

Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV

“…Numerous studies have been carried out indicating a high diversity among R. solani infecting mycoviruses [17][18][19][20]. However, only a small number of different species has been characterized so far, including species of the Partitiviridae, Endornaviridae, Narnaviridae and a few unclassified mycoviruses [21][22][23][24][25][26][27][28]. Deep sequencing analysis, especially of viral metagenomes, is currently the most efficient way to identify unknown viruses.…”