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A significant number of mycoviruses have been identified that are related to plant viruses, but their evolutionary relationships are largely unexplored. A fusarivirus, Rhizoctonia solani fusarivirus 4 (RsFV4), was identified in phytopathogenic fungus Rhizoctonia solani (R. solani) strain XY74 co-infected by an alphaendornavirus. RsFV4 had a genome of 10,833 ​nt (excluding the poly-A tail), and consisted of four non-overlapping open reading frames (ORFs). ORF1 encodes an 825 aa protein containing a conserved helicase domain (Hel1). ORF3 encodes 1550 aa protein with two conserved domains, namely an RNA-dependent RNA polymerase (RdRp) and another helicase (Hel2). The ORF2 and ORF4 likely encode two hypothetical proteins (520 and 542 aa) with unknown functions. The phylogenetic analysis based on Hel2 and RdRp suggest that RsFV4 was positioned within the fusarivirus group, but formed an independent branch with three previously reported fusariviruses of R. solani. Notably, the Hel1 and its relatives were phylogenetically closer to helicases of potyviruses and hypoviruses than fusariviruses, suggesting fusarivirus Hel1 formed an evolutionary link between these three virus groups. This finding provides evidence of the occurrence of a horizontal gene transfer or recombination event between mycoviruses and plant viruses or between mycoviruses. Our findings are likely to enhance the understanding of virus evolution and diversity.

The Arabidopsis thaliana ASYMMETRIC LEAVES2 (AS2) gene is responsible for the development of flat, symmetric, and extended leaf laminae and their veins. The AS2 gene belongs to the plant-specific AS2-LIKE/LATERAL ORGAN BOUNDARIES (LOB)-domain (ASL/LBD), which consists of 42 proteins in Arabidopsis with a conserved amino-terminal domain known as the AS2/LOB domain, and a variable carboxyl-terminal region. AS2/LOB domain consists of an amino-terminal (N-terminal) that contains a cysteine repeat (the C-motif), a conserved glycine residue, and a leucine-zipper-like. AS2/LOB domain has been characterised in plants such as A. thaliana, Zea mays, and Oryza sativum. Nevertheless, it remains uncharacterised in cassava (Manihot esculenta). Characterisation and identification of cassava ASL/LBD genes using the computational algorithms, hidden Markov model profiles (PF03195), determined 55 ASL/LBD genes (MeASLBD1 to MeASLBD55). The gene structure and motif composition were conserved in MeASLBDs, while the expression profiles of these genes were highly diverse, implying that they are associated with diverse functions. Weighted gene co-expression network analysis (WGCNA) of target genes and promoter analysis suggest that these MeASLBDs may be involved in hormone and stress responses. Furthermore, the analysis of cis-regulatory elements in promoter regions suggested that MeASLBDs may be involved in the plant phytohormone signal response. The transcriptome data of cassava under biotic and abiotic stresses revealed that MeASLBD46 and MeASLBD47 greatly respond to disease and drought. The MeASLBD47 gene was selected for functional analysis. The result indicated that MeASLBD47 significantly mitigated the virulence of cassava bacterial blight (XamCHN11) through Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and Virus-induced gene silencing (VIGS). These findings provided a comprehensive analysis of ASL/LBD genes and laid the groundwork for future research to understand ASL/LBD genes.

The phytohormone auxin plays a pivotal role in regulating plant growth, development, and abiotic stress responses by promptly controlling the expression of auxin response genes. The Gretchen Hagen3 (GH3) genes are a major early auxin response gene family that contribute to auxin homeostasis by conjugating excess auxins to amino acids. To our knowledge, a genome-wide investigation of the GH3 genes in alfalfa has never been reported. Here, we present a comprehensive bioinformatics analysis of the MsGH3 gene family, including chromosomal locations, phylogenetic relationships, gene structures, conserved motifs and Gene Ontology annotation. Interestingly, the analysis revealed 31 MsGH3 genes in the alfalfa genome. These genes were classified phylogenetically into the GH3-I, GH3-II, and GH3-III subgroups. Additionally, the data analysis showed that most MsGH3 genes are tissue specific and responsive to environmental stress-related hormones. Furthermore, the analysis of cis elements and potential biological functions revealed that the MsGH3 genes play potential roles in various stress responses. Notably, qRT-PCR results following exposure to high temperature, drought, and salt treatments demonstrated that most of the MsGH3 family genes, especially MsGH3-12, MsGH3-13, and MsGH3-15, play important roles in stress responses. These findings provide invaluable insight for future practical analyses and genetic improvement of alfalfa abiotic stress tolerance.

Streptobotrys caulophylli is a pathogenic fungus that causes leaf and stem blight in many plants. We report a novel fusagravirus identified in S. caulophylli strain STB-2, provisionally named "Streptobotrys caulophylli fusagravirus 1" (ScFV1). The full-length genome of ScFV1 is 9270 nucleotides (nt) long and putatively possesses two large open reading frames (ORF1 and ORF2), which are separated by an intergenic region of 955 nt. A conserved domain search revealed that ORF2 (1051 aa) encodes a putative RNA-dependent RNA polymerase (RdRp), whereas ORF1 (1404 aa) encodes a protein of unknown function. Homology searches and phylogenetic analysis of the putative RdRp suggest that ScFV1 is a new member of the proposed family "Fusagraviridae". This is the first report of a mycovirus infecting the fungus S. caulophylli.

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.

Nidovirales, which accommodates viruses with the largest RNA genomes, includes the notorious coronaviruses; however, the evolutionary route for nidoviruses is not well understood. We have characterized a positive-sense (+) single-stranded (ss) RNA mycovirus, Rhizoctonia solani hypovirus 2 (RsHV2), from the phytopathogenic fungus Rhizoctonia solani. RsHV2 has the largest RNA genome size of 22,219 nucleotides, excluding the poly(A) tail, in all known mycoviruses, and contains two open reading frames (ORF1 and ORF2). ORF1 encodes a protein of 2,009 amino acid (aa) that includes a conserved helicase domain belonging to helicase superfamily I (SFI). In contrast, ORF2 encodes a polyprotein of 4459 aa containing the hallmark genes of hypoviruses. The latter includes a helicase belonging to SFII. Following phylogenetic analysis, the ORF1-encoded helicase (Hel1) unexpectedly clustered in an independent evolutionary branch together with nidovirus helicases, including coronaviruses, and bacteria helicases. Thus, Hel1 presence indicates the occurrence of horizontal gene transfer between viruses and bacteria. These findings also suggest that RsHV2 is most likely a recombinant arising between hypoviruses and nidoviruses.

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.

A double-stranded RNA (dsRNA) segment was isolated from the filamentous phytopathogenic fungus Rhizoctonia oryzae-sativae and its full-length cDNA sequence (3038 nucleotides) was determined. Sequence analysis revealed that a large open reading frame (ORF) is present on the positive strand of this dsRNA segment when the mitochondrial genetic code was applied. The ORF encodes a putative RNA-dependent RNA polymerase, which shares the closest similarity with Rhizoctonia mitovirus 1 and Rhizophagus sp. RF1 mitovirus, with 43% and 29% identity, respectively. This dsRNA segment represents the replication form of a novel mitovirus that was temporarily designated Rhizoctonia oryzae-sativae mitovirus 1 (RoMV1). Phylogenetic analysis further suggested that RoMV1 belongs to the family Narnaviridae. This is the first study to report a mitovirus genome sequence in the phytopathogenic fungus R. oryzae-sativae.