Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents

Abstract

Macrophomina phaseolina is an important necrotrophic phytopathogenic fungus and cause extensive damage in many oilseed crops. Twelve M.phaseolina isolates with diverse biological phenotypes were selected for a high-throughput sequencing-based metatranscriptomic and bioinformatics analysis to identify viruses infecting M.phaseolina . The analysis identified 40 partial or nearly complete viral genome segments, 31 of which were novel viruses. Among these viral sequences, 43% of the viral genomes were double-stranded RNA (dsRNA), 47% were positive single-stranded RNA (ssRNA+), and the remaining 10% were negative sense-stranded RNA (ssRNA−). The 40 viruses showed affinity to 13 distinct viral lineages, including Bunyavirales (four viruses), Totiviridae (three viruses), Chrysoviridae (five viruses), Partitiviridae (four viruses), Hypoviridae (one virus), Endornaviridae (two viruses), Tombusviridae (three viruses), Narnaviridae (one virus), Potyviridae (one virus), Bromoviridae (one virus), Virgaviridae (six viruses), ‘Fusagraviridae’ (five viruses), and Ourmiavirus (four viruses). Two viruses are closely related to two families, Potyviridae and Bromoviridae , which previously contained no mycovirus species. Moreover, nine novel viruses associated with M.phaseolina were identified in the family Totiviridae , Endornaviridae , and Partitiviridae . Coinfection with multiple viruses is prevalent in M.phaseolina , with each isolate harboring different numbers of viruses, ranging from three to eighteen. Furthermore, the effects of the viruses on the fungal host were analyzed according to the biological characteristics of each isolate. The results suggested that M.phaseolina hypovirus 2, M.phaseolina fusagravirus virus 1-5 (MpFV1-5), M.phaseolina endornavirus 1-2 (MpEV1-2), M.phaseolina ourmia-like virus 1-3 (MpOLV1-3), M.phaseolina mitovirus 4 (MpMV4), and M.phaseolina mycobunyavirus 1-4 (MpMBV1-4) were only detected in hypovirulent isolates. Those viruses associated with hypovirulence might be used as biological control agents as an environmentally friendly alternative to chemical fungicides. These findings considerably expand our understanding of mycoviruses in M.phaseolina and unvailed the presence of a huge difference among viruses in isolates from different hosts in distant geographical regions. Together, the present study provides new knowledge about...

A New Double-Stranded RNA Mycovirus in <em>Cryphonectria naterciae</em> is Able to Cross the Species Barrier and is Deleterious to a New Host

“…The 5'-UTR is with 757 nt much longer than the 3'-UTR of 45 nt length. However, a protein search at CDD confirmed that the predicted ORF2 protein contains a RdRp domain (RdRp_4; pfam02123; Cd length: 465), exhibiting conserved motif characteristics detected in members of the proposed Fusagraviridae members in former studies (e.g., Fusarium poae dsRNA virus 2 and 3 [13], Trichoderma asperellum dsRNA virus 1 [55], or Macrophomina phaseolina fusagravirus 2-5 [56]), but also in other dsRNA viral families, such as Colletotrichum fructicola chrysovirus 1 [57] or Macrophomina phaseolina chrysovirus 2 RNA1 [56]. The similarity in the RdRp region supported additionally that the M10544-dsRNA is a dsRNA fusagravirus.…”

“…This study revealed that 13/31 (c. 40%) of C. naterciae strains harbour a unique dsRNA virus named Cryphonectria naterciae fusagravirus 1 (CnFGV1). The complete CnFGV1-genome derived from strain M10544 consists of 10,161 nt, which possesses two ORFs-ORF1 and ORF2-of which ORF2 is situated in -1 frame relative to ORF1, as found for many other dsRNA mycoviruses within the order Ghabrivirales [13,[55][56][57][58][59]61]. Amino acid sequence analyses showed moderate levels of sequence identity of ORF1 and ORF2 to the counterparts of dsRNA viruses such as Fusarium virguliforme dsRNA mycovirus [58] and Trichoderma atroviride mycovirus [59] of the previously proposed viral family Fusagraviridae.…”

“…Sectoring has been reported as a common symptom caused by mycoviruses due to alteration of physiological and biochemical processes in fungi [27]. High-density sectors have been described for other fungi in relation with mycovirus infection, e.g., Beauveria bassiana [62], Colletotrichum fructicola [57], Macrophomina phaseolina [56], or Fusarium equiseti [63], and have also been mentioned in the context of decreasing virus titre [64]. In contrast to other studies, the present work used genetically diverse fungal isolates (Supplementary Table S5), and we assume that different strains may respond differently to a viral invasion, which probably is represented in varying degree of debilitation.…”

Transcriptional Responses of Sclerotinia sclerotiorum to the Infection by SsHADV-1

“…Mycovirus-induced hypovirulence could be found in many important plant hemi-biotrophic and necrotrophic pathogenic fungi, including Aspergillus spp., Alternaria alternata , Bipolaris maydis , Botryosphaeria dothidea , Botrytis spp., Cryphonectria parasitica , Colletotrichum spp., Diaporthe spp., Fusarium spp., Helicobasidium mompa , Helminthosporium victoriae , Heterobasidion annosum , Macrophomina phaseolina , Magnaporthe oryzae , Ophiostoma spp., Penicillium digitatum , Pestalotiopsis theae , Rosellinia necatrix , Rhizoctonia solani , Sclerotinia spp. and so on [ 3 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ], indicating hypovirulence-related mycoviruses as potential resources to control plant fungal diseases [ 4 ].…”

Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome

“…Sometimes, lab isolates of fungal cultures have sectoring growth and are discarded by the pathologists when the transferred isolates grow slowly and become hard to maintain. Therefore, candidates of biopesticide or biotechnological use could be eliminated in the culturing/serial passage process, e.g., Macrophomina phaseolina tobamo -like virus 1 [ 11 , 14 ]. Moreover, some fungal pathogens, e.g., sunflower downy mildew and rust, being obligate parasites, cannot be cultured in the lab.…”