The cosmopolitan fungus Rhizoctonia solani has a wide host range and is the causal agent of numerous crop diseases, leading to significant economic losses. To date, no cultivars showing complete resistance to R. solani have been identified and it is imperative to develop a strategy to control the spread of the disease. Fungal viruses, or mycoviruses, are widespread in all major groups of fungi and next-generation sequencing (NGS) is currently the most efficient approach for their identification. An increasing number of novel mycoviruses are being reported, including double-stranded (ds) RNA, circular single-stranded (ss) DNA, negative sense (−)ssRNA, and positive sense (+)ssRNA viruses. The majority of mycovirus infections are cryptic with no obvious symptoms on the hosts; however, some mycoviruses may alter fungal host pathogenicity resulting in hypervirulence or hypovirulence and are therefore potential biological control agents that could be used to combat fungal diseases. R. solani harbors a range of dsRNA and ssRNA viruses, either belonging to established families, such as Endornaviridae, Tymoviridae, Partitiviridae, and Narnaviridae, or unclassified, and some of them have been associated with hypervirulence or hypovirulence. Here we discuss in depth the molecular features of known viruses infecting R. solani and their potential as biological control agents.

Various mycoviruses have been isolated from Sclerotinia sclerotiorum. Here, we identified a viral RNA sequence contig, representing a novel virus, Sclerotinia sclerotiorum deltaflexivirus 2 (SsDFV2), from an RNA_Seq database. We found that SsDFV2 was harbored in the hypovirulent strain, 228, which grew slowly on potato dextrose agar, produced a few sclerotia, and could not induce typical lesions on detached rapeseed (Brassica napus) leaves. Strain 228 was also infected by Botrytis porri RNA Virus 1 (BpRV1), a virus originally isolated from Botrytis porri. The genome of SsDFV2 comprised 6711 nucleotides, excluding the poly (A) tail, and contained a single large predicted open reading frame encoding a putative viral RNA replicase. Phylogenetic analysis demonstrated that SsDFV2 is closely related to viruses in the family Deltaflexiviridae; however, it also differs significantly from members of this family, suggesting that it may represent a new species. Further we determined that SsDFV2 could be efficiently transmitted to host vegetative incompatible individuals by dual culture. To our best knowledge, this is the first report that a (+) ssRNA mycovirus can overcome the transmission limitations of the vegetative incompatibility system, a phenomenon that may facilitate the potential use of mycoviruses for the control of crop fungal diseases.

Codon usage bias (CUB) could reflect co-evolutionary changes between viruses and hosts in contrast to plant and animal viruses, and the systematic analysis of codon usage among the mycoviruses that infect plant pathogenic fungi is limited. We performed an extensive analysis of codon usage patterns among 98 characterized RNA mycoviruses from eight phytopathogenic fungi. The GC and GC3s contents of mycoviruses have a wide variation from 29.35% to 64.62% and 24.32% to 97.13%, respectively. Mycoviral CUB is weak, and natural selection plays a major role in the formation of mycoviral codon usage pattern. In this study, we demonstrated that the codon usage of mycoviruses is similar to that of some host genes, especially those involved in RNA biosynthetic process and transcription, suggesting that CUB is a potential evolutionary mechanism that mycoviruses adapt to in their hosts.

In pursuing higher rice production, we have often jeopardized soil at an alarming rate. It is hypothesized that intensive farming practices degrade soil health and increase the abundance of rice diseases while fallowing increases the abundance of biocontrol agents. In this study, the bacterial community was monitored in the paddy and fallow soil. Proteobacteria, Bacteroidetes, and Actinobacteria were abundant in the fallow soil, whereas Acidobacteria, Chloroflexi, and Gemmatimonadetes were more abundant in the paddy soil. Among the potential biocontrol agents, Bacillus, Thiobacillus, Rhizobium, Massilia, Rhizobacter, Streptomyces, Micromonospora, and Pseudonocardia were more abundant in the fallow soil, while Pseudomonas and Burkholderia were more abundant in the paddy soil. The possible rice pathogens, i.e., Xanthomonas and Erwinia, were more abundant in the paddy soil. The alpha diversity was higher in paddy soil than in fallow soil. Additionally, the principal coordinate analysis based on UniFrac distances revealed distinct clusters of the soils. Moreover, the functional analysis suggested that the fallow soil was abundant in genes associated with the biosynthesis of siderophores and secondary metabolites. In contrast, the paddy soil was abundant in genes related to plant-pathogen interactions. In conclusion, these results highlight the significance of fallowing to improve soil health.

MicroRNAs (miRNAs) are a class of noncoding RNAs that play important roles in regulating gene expression. They are involved in various biological processes, including plant growth, development, hormone signalling pathways and defence responses. Numerous studies have demonstrated the crucial role of miRNA in modulating plant immunity against various pathogens, including fungi, bacteria, viruses, nematodes and oomycetes. In this review, we synthesise recent advances in defence‐related miRNAs in response to pathogens, highlighting their effects on plant–pathogen interactions and their functions in regulating hormone signalling pathways. Additionally, we explore the potential of small RNA‐based technology tools in protecting plants from pathogens, including artificial microRNA, synthetic trans‐acting small interfering RNA and RNA interference techniques, such as spray‐induced gene silencing, host‐induced gene silencing and virus‐induced gene silencing.

Studies have demonstrated microRNA398 (miR398) hyperaccumulation in plant species infected with viruses; however, its role in a viral context remains unexplored. Here, we identified cassava (Mes)‐miR398 as a regulatory miRNA responsive to cassava common mosaic virus (CsCMV) infection through small‐RNA analysis. Mes‐miR398 targets Dirigent (Dir; Manes.05G165700.1) associated with disease resistance. Transgenic cassava lines overexpressing Mes‐miR398 (OE398) showed downregulation of the Dir gene during CsCMV infection. A dual‐luciferase reporter assay confirmed the direct targeting of the Dir gene by miR398. Interestingly, OE398 lines exhibited enhanced vegetative growth. However, CsCMV accumulation was significantly higher in OE398‐CsCMV and Dir ‐silenced (SDir)‐CsCMV lines and reduced in Dir ‐overexpressing (OEDir‐CsCMV) lines, indicating a negative regulatory role of the Mes‐miR398/Dir module in antiviral defence. Transmission electron microscopy revealed a reduction in cell wall thickness in CsCMV‐infected plants compared with healthy controls. A similar decrease was observed in SDir lines, whereas OEDir lines maintained greater wall thickness. Furthermore, lignin content was significantly reduced in SDir lines relative to OEDir lines. Histochemical staining with Toluidine Blue O and Safranin O−Fast Green supported these findings, showing increased lignification in OEDir lines and reduced lignification in SDir lines. Subcellular localisation demonstrated that the Dir protein localises to the cell membrane, suggesting a role in regulating the cell wall membrane. These results revealed that the mes‐miR398/Dir regulatory module negatively affects cassava resistance to CsCMV by altering cell wall lignification. This study is the first to identify miR398 as a regulator of a Dir gene and provides critical insights into the molecular interactions between cassava and CsCMV.