Diversity of Mycoviruses Present in Strains of Binucleate Rhizoctonia and Multinucleate Rhizoctonia, Causal Agents for Potato Stem Canker or Black Scurf

Abstract

In this study, the diversity of putative mycoviruses present in 66 strains of binucleate Rhizoctonia (BNR, including anastomosis group (AG)-A, AG-Fa, AG-K, and AG-W) and 192 strains of multinucleate Rhizoctonia (MNR, including AG-1-IA, AG-2-1, AG-3 PT, AG-4HGI, AG-4HGII, AG-4HGIII, and AG-5), which are the causal agents of potato stem canker or black scurf, was studied using metatranscriptome sequencing. The number of contigs related to mycoviruses identified from BNR and MNR was 173 and 485, respectively. On average, each strain of BNR accommodated 2.62 putative mycoviruses, while each strain of MNR accommodated 2.53 putative mycoviruses. Putative mycoviruses detected in both BNR and MNR contained positive single-stranded RNA (+ssRNA), double-stranded RNA (dsRNA), and negative single-stranded RNA (-ssRNA) genomes, with +ssRNA genome being the prevalent nucleic acid type (82.08% in BNR and 75.46% in MNR). Except for 3 unclassified, 170 putative mycoviruses found in BNR belonged to 13 families; excluding 33 unclassified, 452 putative mycoviruses found in MNR belonged to 19 families. Through genome organization, multiple alignments, and phylogenetic analyses, 4 new parititviruses, 39 novel mitoviruses, and 4 new hypoviruses with nearly whole genome were detected in the 258 strains of BNR and MNR.

Anastomosis Groups and Mycovirome of Rhizoctonia Isolates Causing Sugar Beet Root and Crown Rot and Their Sensitivity to Flutolanil, Thifluzamide, and Pencycuron

“…Viruses of the family Mitoviridae are known to be the simplest naked mycoviruses and exist as RNA-RdRp nucleoprotein complexes, whose genomes only encode an RdRp protein [28]. In the present study, 37 mitoviruses predicted to have a complete ORF were divided into three clades (clade I, clade II, and clade III) in the phylogenetic tree (Figure 3), whose aa sequence identities of RdRp with those of the corresponding mitoviruses in the NCBI Nr database ranged from 39.83% to 89.66%; moreover, the result of phylogenetic analysis is consistent with that of the previous reports [37,46,60,61].…”

“…The sequences which could encode an ORF that begins at the start codon and ends at the termination codon, were predicted to contain a complete ORF. Then, Conserved Domain Database (CDD) (with e-value of 0.01) (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, accessed on 8 January 2021), Protein Family (Pfam) database (http://pfam.sanger.ac.uk/, accessed on 8 January 2021), and PROSITE database (http://www.expasy.ch/, accessed on 8 January 2021) were used to find conserved motifs of amino acid (aa) sequences of putative mycoviruses [37,46,52]. CLUSTAL_X was used to perform sequence alignments [53].…”

“…The name of a novel putative mycovirus identified for the first time in this study is named according to previous references [46,55], which consists of three parts: (1) the first part is the source of the virus; (2) the second part shows the virus taxonomical group; and (3) the third part is a progressive number. For example, "Rhizoctonia solani [part 1] mitovirus [part 2] 41 [part 3]" presents a new mitovirus and the forty-first mitovirus found in R. solani.…”

“…A metatranscriptomic analysis of 43 isolates of R. solani AG-1-IA infecting rice that sampled in southern China was performed, and 10 mycovirus-related contigs compos-ing five mycoviruses were obtained [45]. Recently, the diversity of putative mycoviruses containing +ssRNA, dsRNA, and -ssRNA genomes present in 66 strains of BNR (including AG-A, AG-Fa, AG-K, and AG-W) and 192 strains of MNR (including AG-1-IA, AG-2-1, AG-3 PT, AG-4HGI, AG-4HGII, AG-4HGIII, and AG-5) inciting potato stem canker or black scurf was studied using metatranscriptome sequencing, with four new parititviruses, 39 novel mitoviruses, and four new hypoviruses with nearly whole genome being detected in these 258 strains of BNR and MNR [46].…”

“…Until now, there are no detailed reports related to AGs or subgroups composition of Rhizoctonia isolates associated with sugar beet root and crown rot across China, let alone the diversity of mycoviruses present in these Rhizoctonia isolates as well as the sensitivity of them to the three fungicides (flutolanil, thifluzamide, and pencycuron). In the current study, the AGs or subgroups composition of Rhizoctonia isolates associated with sugar beet root and crown rot were characterized based on morphological traits and sequence analysis of internal transcribed spacer region of ribosomal DNA (rDNA-ITS) [10], the diversity of mycoviruses infecting these Rhizoctonia isolates were explored and analyzed by metatranscriptome sequencing [46], and the sensitivity of these Rhizoctonia isolates to the three fungicides (flutolanil, thifluzamide, and pencycuron) was detected using the mycelium growth inhibition method [23,24,47]. The results obtained in this study will be of great significance for understanding the AGs or subgroups composition of Rhizoctonia causing sugar beet rot and crown rot, revealing the diversity of mycoviruses discovered in Rhizoctonia, and screening efficient fungicides used for controlling diseases caused by Rhizoctonia.…”