Complete nucleotide sequence of a new double-stranded RNA virus from the rice blast fungus, Magnaporthe oryzae

Metatranscriptomic Analysis Reveals Rich Mycoviral Diversity in Three Major Fungal Pathogens of Rice

In recent years, three major fungal diseases of rice, i.e., rice blast, rice false smut, and rice-sheath blight, have caused serious worldwide rice-yield reductions and are threatening global food security. Mycoviruses are ubiquitous in almost all major groups of filamentous fungi, oomycetes, and yeasts. To reveal the mycoviral diversity in three major fungal pathogens of rice, we performed a metatranscriptomic analysis of 343 strains, representing the three major fungal pathogens of rice, Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, sampled in southern China. The analysis identified 682 contigs representing the partial or complete genomes of 68 mycoviruses, with 42 described for the first time. These mycoviruses showed affinity with eight distinct lineages: Botourmiaviridae, Partitiviridae, Totiviridae, Chrysoviridae, Hypoviridae, Mitoviridae, Narnaviridae, and Polymycoviridae. More than half (36/68, 52.9%) of the viral sequences were predicted to be members of the families Narnaviridae and Botourmiaviridae. The members of the family Polymycoviridae were also identified for the first time in the three major fungal pathogens of rice. These findings are of great significance for understanding the diversity, origin, and evolution of, as well as the relationship between, genome structures and functions of mycoviruses in three major fungal pathogens of rice.

Molecular characterization of a novel botourmiavirus with inverted complementary termini from the rice blast fungus Magnaporthe oryzae isolate HF04

A novel positive-sense single-stranded RNA mycovirus, designated as "Magnaporthe oryzae botourmiavirus 10" (MoBV10), was identified in the rice blast fungus Magnaporthe oryzae isolate HF04. MoBV10 has a single genomic RNA segment consisting of 2,448 nucleotides, which contains a single open reading frame encoding an RNA-dependent RNA polymerase. Genome comparison and phylogenetic analysis indicated that MoBV10 is a new member of the genus Betascleroulivirus in the family Botourmiaviridae. The 5'- and 3'-terminal sequences of the genomic RNA of MoBV10 have inverted complementarity and potentially form a panhandle structure, which is very rare in RNA viruses.

Complete nucleotide sequence of a novel botourmiavirus from the rice blast fungus Magnaporthe oryzae isolate SH05

A novel mycovirus with the proposed name "Magnaporthe oryzae botourmiavirus 9" (MoBV9) was found in the rice blast fungus Magnaporthe oryzae isolate SH05. The virus has a positive single-stranded RNA genome of 2,812 nucleotides and contains a single open reading frame predicted to encode an RNA-dependent RNA polymerase that is closely related to those of some unclassified viruses of the family Botourmiaviridae, including Plasmopara viticola lesion associated ourmia-like virus 44, Plasmopara viticola lesion associated ourmia-like virus 47, and Cladosporium uredinicola ourmiavirus 1. Genome sequence comparisons and phylogenetic analysis supported the notion that MoBV9 is a new member of the family Botourmiaviridae.

Four Novel Botourmiaviruses Co-Infecting an Isolate of the Rice Blast Fungus Magnaporthe oryzae

Via virome sequencing, six viruses were detected from Magnaporthe oryzae strains YC81-2, including one virus in the family Tombusviridae, one virus in the family Narnaviridae and four viruses in the family Botourmiaviridae. Since the RNA-dependent RNA polymerase (RdRp) of one botourmiavirus show the highest identity (79%) with Magnaporthe oryzae ourmia-like virus 1 (MOLV1), the virus that was grouped into the genus Magoulivirus was designated as Magnaporthe oryzae botourmiavirus 2 (MOBV2). The three other novel botourmiaviruses were selected for further study. The complete nucleotide sequences of the three botourmiaviruses were determined. Sequence analysis showed that virus 1, virus 2, and virus 3 were 2598, 2385, and 2326 nts in length, respectively. The variable 3' untranslated region (3'-UTR) and 5'-UTR of each virus could be folded into a stable stem-loop secondary structure. Each virus consisted of a unique ORF encoding a putative RdRp. The putative proteins with a conserved GDD motif of RdRp showed the highest sequence similarity to RdRps of viruses in the family Botourmiaviridae. Phylogenetic analysis demonstrated that these viruses were three distinct novel botourmiaviruses, clustered into the Botourmiaviridae family but not belonging to any known genera of this family. Thus, virus 1, virus 2, and virus 3 were designated as Magnaporthe oryzae botourmiavirus 5, 6, and 7 (MOBV5, MOBV6, and MOBV7), respectively. Our results suggest that four distinct botourmiaviruses, MOBV2, MOBV5, MOBV6, and MOBV7, co-infect a single strain of Magnaporthe oryzae, and MOBV5, MOBV6, and MOBV7 are members of three unclassified genera in the family Botourmiaviridae.

Population Structure of Double-Stranded RNA Mycoviruses That Infect the Rice Blast Fungus Magnaporthe oryzae in Japan

Various viruses infect Magnaporthe oryzae (syn. Pyricularia oryzae), which is a well-studied fungus that causes rice blast disease. Most research has focused on the discovery of new viruses and the hypovirulence-associated traits conferred by them. Therefore, the diversity and prevalence of viruses in wild fungal populations have not been explored. We conducted a comprehensive screening of M. oryzae mycoviruses from various regions in Japan using double-stranded RNA (dsRNA) electrophoresis and RT-PCR assays. We detected three mycoviruses, Magnaporthe oryzae virus 2 (MoV2), Magnaporthe oryzae chrysovirus 1 (MoCV1), and Magnaporthe oryzae partitivirus 1 (MoPV1), among 127 of the 194 M. oryzae strains screened. The most prevalent virus was MoPV1 (58.8%), which often co-infected in a single fungal strain together with MoV2 or MoCV1. MoV2 and MoCV1 were found in 22.7 and 10.8% of strains, respectively, and they were usually distributed in different regions so that mixed-infection with these two mycoviruses was extremely rare. The predominance of MoPV1 in M. oryzae is supported by significant negative values from neutrality tests, which indicate that the population size of MoPV1 tends to increase. Population genetic analyses revealed high nucleotide diversity and the presence of phylogenetically diverse subpopulations among the MoV2 isolates. This was not the case for MoPV1. Furthermore, studies of a virus-cured M. oryzae strain revealed that MoV2 does not cause any abnormalities or symptoms in its host. However, a leaf sheath inoculation assay showed that its presence slightly increased the speed of mycelial growth, compared with virus-free mycelia. These results demonstrate that M. oryzae in Japan harbors diverse dsRNA mycovirus communities with wide variations in their population structures among different viruses.

A novel narnavirus from the plant-pathogenic fungus Magnaporthe oryzae

A novel mycovirus with the proposed name "Magnaporthe oryzae narnavirus virus 1" (MoNV1), was described in the rice blast fungus Magnaporthe oryzae. The virus has a single-stranded (+ss) RNA genome of 2452 nucleotides, contains a single open reading frame (ORF) predicted to encode an RNA-dependent RNA polymerase (RDRP), and is closely related to some viruses of the genus Narnavirus, family Narnaviridae, including Aspergillus fumigatus narnavirus 1 (AfNV1), Neofusicoccum parvum narnavirus 2 (NpNV2) and Alternaria tenuissima narnavirus 1 (AtNV2). Genome sequence comparisons and phylogenetic analysis suggested that MoNV1 is a new member of the genus Narnavirus. The RDRPs of MoNV1 and some closely related narnaviruses do not contain a typical metal-binding "GDD" motif and catalytic site. Further studies are needed to investigate the replication mechanism of these viruses.

Chrysoviruses in Magnaporthe oryzae

Magnaporthe oryzae, the fungus that causes rice blast, is the most destructive pathogen of rice worldwide. A number of M. oryzae mycoviruses have been identified. These include Magnaporthe oryzae. viruses 1, 2, and 3 (MoV1, MoV2, and MoV3) belonging to the genus, Victorivirus, in the family, Totiviridae; Magnaporthe oryzae. partitivirus 1 (MoPV1) in the family, Partitiviridae; Magnaporthe oryzae. chrysovirus 1 strains A and B (MoCV1-A and MoCV1-B) belonging to cluster II of the family, Chrysoviridae; a mycovirus related to plant viruses of the family, Tombusviridae (Magnaporthe oryzae. virus A); and a (+)ssRNA mycovirus closely related to the ourmia-like viruses (Magnaporthe oryzae. ourmia-like virus 1). Among these, MoCV1-A and MoCV1-B were the first reported mycoviruses that cause hypovirulence traits in their host fungus, such as impaired growth, altered colony morphology, and reduced pigmentation. Recently we reported that, although MoCV1-A infection generally confers hypovirulence to fungi, it is also a driving force behind the development of physiological diversity, including pathogenic races. Another example of modulated pathogenicity caused by mycovirus infection is that of Alternaria alternata chrysovirus 1 (AaCV1), which is closely related to MoCV1-A. AaCV1 exhibits two contrasting effects: Impaired growth of the host fungus while rendering the host hypervirulent to the plant, through increased production of the host-specific AK-toxin. It is inferred that these mycoviruses might be epigenetic factors that cause changes in the pathogenicity of phytopathogenic fungi.

Vírus que infectam fungos fitopatogênicos

RESUMO: Micovírus são vírus que infectam todos os taxa de fungos. São geralmente crípticos (latentes), mas podem causar pequenas ou imperceptíveis alterações no hospedeiro. Nos fungos fitopatogênicos, os vírus podem interferir com os sintomas e, em alguns casos, reduzir a virulência de seu hospedeiro; por esta razão, são objeto de estudo, por serem um potencial agente de biocontrole e por serem ferramentas importantes para o conhecimento sobre os mecanismos de patogênese de fungos. A presente revisão teve o objetivo de reunir os dados de literatura relacionados aos aspectos gerais da biologia e do comportamento dos micovírus presentes em alguns fungos fitopatogênicos.

Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae

In this study we characterize a novel positive and single stranded RNA (ssRNA) mycovirus isolated from the rice field isolate of Magnaporthe oryzae Guy11. The ssRNA contains a single open reading frame (ORF) of 2,373 nucleotides in length and encodes an RNA-dependent RNA polymerase (RdRp) closely related to ourmiaviruses (plant viruses) and ourmia-like mycoviruses. Accordingly, we name this virus Magnaporthe oryzae ourmia-like virus 1 (MOLV1). Although phylogenetic analysis suggests that MOLV1 is closely related to ourmia and ourmia-like viruses, it has some features never reported before within the Ourmiavirus genus. 3' RLM-RACE (RNA ligase-mediated rapid amplification of cDNA ends) and extension poly(A) tests (ePAT) suggest that the MOLV1 genome contains a poly(A) tail whereas the three cytosine and the three guanine residues present in 5' and 3' untranslated regions (UTRs) of ourmia viruses are not observed in the MOLV1 sequence. The discovery of this novel viral genome supports the hypothesis that plant pathogenic fungi may have acquired this type of viruses from their host plants.

Genome sequence of a novel victorivirus identified in the phytopathogenic fungus Alternaria arborescens

Strains of the phytopathogenic fungus Alternaria spp. have been found to contain a variety of double-stranded RNA (dsRNA) elements indicative of mycovirus infection. Here, we report the molecular characterization of a novel dsRNA mycovirus, Alternaria arborescens victorivirus 1 (AaVV1), from A. arborescens, the tomato pathotype of A. alternata. Using next-generation sequencing of dsRNA purified from an A. arborescens strain from the United States of America, we found that the AaVV1 genome is 5203 bp in length and contains two open reading frames (ORF1 and 2) that overlap at the tetranucleotide AUGA. Proteins encoded by ORF1 and ORF2 showed significant similarities to the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp), respectively, of dsRNA mycoviruses of the genus Victorivirus. Pairwise comparisons and phylogenetic analysis of the deduced amino acid sequences of both CP and RdRp indicated that AaVV1 is a member of a distinct species of the genus Victorivirus in the family Totiviridae.

A novel single-stranded RNA virus isolated from the rice-pathogenic fungus Magnaporthe oryzae with similarity to members of the family Tombusviridae

Here, we report a novel virus isolated from rice blast fungus, Magnaporthe oryzae, an important plant pathogen. This virus has an RNA genome of 3246 nucleotides. Its genome possesses two in-frame open reading frames (ORFs). The smaller ORF1 encodes a protein with significant similarity to a protein encoded by the ssRNA mycovirus Diaporthe ambigua RNA virus 1 (DaRV1). The larger ORF2 encodes a protein with similarity to RNA-dependent RNA polymerases (RdRp) of DaRV1 and other plant viruses of the family Tombusviridae. In silico analysis and comparisons with DaRV1 genome expression suggest that ORF2 is translated via a readthrough mechanism together with ORF1. Based upon results of this study, this virus, for which the provisional name Magnaporthe oryzae virus A (MoVA) is proposed, belongs to a new virus species. Furthermore, MoVA along with DaRV1 belong to a new taxon of mycoviruses that are evolutionarily related to plant viruses belonging to the family Tombusviridae.

Detection of Magnaporthe oryzae chrysovirus 1 in Japan and establishment of a rapid, sensitive and direct diagnostic method based on reverse transcription loop-mediated isothermal amplification

Magnaporthe oryzae chrysovirus 1 (MoCV1) is a mycovirus with a dsRNA genome that infects the rice blast fungus Magnaporthe oryzae and impairs its growth. To date, MoCV1 has only been found in Vietnamese isolates of M. oryzae, and the distribution of this virus in M. oryzae isolates from other parts of the world remains unknown. In this study, using a one-step reverse transcription PCR (RT-PCR) assay, we detected a MoCV1-related virus in M. oryzae in Japan (named MoCV1-AK) whose sequence shares considerable similarity with that of the MoCV1 Vietnamese isolate. To establish a system for a comprehensive survey of MoCV1 infection in the field, we developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for direct detection of the virus. The sensitivity of the RT-LAMP assay was at least as high as that of the one-step RT-PCR assay. In addition, we detected MoCV1-AK in M. oryzae-infected oatmeal agar plates and lesions on rice leaves using the RT-LAMP assay without dsRNA extraction, by simple sampling with a toothpick. Preliminary screening of MoCV1 in Japanese M. oryzae isolates indicated that MoCV1 is currently distributed in rice fields in Japan. Our results provide a first example of the application of RT-LAMP for the detection of mycoviruses, which will accelerate surveys for mycovirus infection.

Molecular genetics and Biochemical analyses of mycoviruses in rice blast fungus, Magnaporthe oryzae

We have found a novel mycovirus, MoCV1 in the rice blast fungus, Magnaporthe oryzae. MoCV1 has five dRNA segments as genome, and belong to Chrysoviridae tentatively. Using micro-spin column method or one-step reverse-transcription PCR (RT-PCR) assay, we detected a MoCV1-related virus from M. oryzae in Japan, whose sequence shares considerable identity with that of the MoCV1 Vietnamese isolate. To establish a system for comprehensive survey of MoCV1 infection in the field, we developed a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for direct detection of the virus. In this review, we introduce our current knowledges of MoCV1 properties for biochemical and molecular genetic aspects and also describe its negative effects to host fungus, which imply potentiality to utilize MoCV1 as bio-controller. Heterologous gene-expression system in yeast is employed to investigate biological activities or functions of mycoviral proteins in fungal host cells. MoCV1-A infection caused hypovirulence to the host fungus, unexpectedly, also resulted in the change of pathogenic races in several differential rice lines, namely S (compatible) to R (incompatible) reaction or R to S. The cause of epigenetic alteration is also discussed.

New insights into mycoviruses and exploration for the biological control of crop fungal diseases

Mycoviruses are viruses that infect fungi. A growing number of novel mycoviruses have expanded our knowledge of virology, particularly in taxonomy, ecology, and evolution. Recent progress in the study of mycoviruses has comprehensively improved our understanding of the properties of mycoviruses and has strengthened our confidence to explore hypovirulence-associated mycoviruses that control crop diseases. In this review, the advantages of using hypovirulence-associated mycoviruses to control crop diseases are discussed, and, as an example, the potential for Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) to control the stem rot of rapeseed (Brassica napus) is also introduced. Fungal vegetative incompatibility is likely to be the key factor that limits the wide utilization of mycoviruses to control crop diseases; however, there are suggested strategies for resolving this problem.

Real time classification of viruses in 12 dimensions

The International Committee on Taxonomy of Viruses authorizes and organizes the taxonomic classification of viruses. Thus far, the detailed classifications for all viruses are neither complete nor free from dispute. For example, the current missing label rates in GenBank are 12.1% for family label and 30.0% for genus label. Using the proposed Natural Vector representation, all 2,044 single-segment referenced viral genomes in GenBank can be embedded in [Formula: see text]. Unlike other approaches, this allows us to determine phylogenetic relations for all viruses at any level (e.g., Baltimore class, family, subfamily, genus, and species) in real time. Additionally, the proposed graphical representation for virus phylogeny provides a visualization of the distribution of viruses in [Formula: see text]. Unlike the commonly used tree visualization methods which suffer from uniqueness and existence problems, our representation always exists and is unique. This approach is successfully used to predict and correct viral classification information, as well as to identify viral origins; e.g. a recent public health threat, the West Nile virus, is closer to the Japanese encephalitis antigenic complex based on our visualization. Based on cross-validation results, the accuracy rates of our predictions are as high as 98.2% for Baltimore class labels, 96.6% for family labels, 99.7% for subfamily labels and 97.2% for genus labels.

Characterization of Magnaporthe oryzae chrysovirus 1 structural proteins and their expression in Saccharomyces cerevisiae

Magnaporthe oryzae chrysovirus 1 (MoCV1), which is associated with an impaired growth phenotype of its host fungus, harbors four major proteins: P130 (130 kDa), P70 (70 kDa), P65 (65 kDa), and P58 (58 kDa). N-terminal sequence analysis of each protein revealed that P130 was encoded by double-stranded RNA1 (dsRNA1) (open reading frame 1 [ORF1] 1,127 amino acids [aa]), P70 by dsRNA4 (ORF4; 812 aa), and P58 by dsRNA3 (ORF3; 799 aa), although the molecular masses of P58 and P70 were significantly smaller than those deduced for ORF3 and ORF4, respectively. P65 was a degraded form of P70. Full-size proteins of ORF3 (84 kDa) and ORF4 (85 kDa) were produced in Escherichia coli. Antisera against these recombinant proteins detected full-size proteins encoded by ORF3 and ORF4 in mycelia cultured for 9, 15, and 28 days, and the antisera also detected smaller degraded proteins, namely, P58, P70, and P65, in mycelia cultured for 28 days. These full-size proteins and P58 and P70 were also components of viral particles, indicating that MoCV1 particles might have at least two forms during vegetative growth of the host fungus. Expression of the ORF4 protein in Saccharomyces cerevisiae resulted in cytological changes, with a large central vacuole associated with these growth defects. MoCV1 has five dsRNA segments, as do two Fusarium graminearum viruses (FgV-ch9 and FgV2), and forms a separate clade with FgV-ch9, FgV2, Aspergillus mycovirus 1816 (AsV1816), and Agaricus bisporus virus 1 (AbV1) in the Chrysoviridae family on the basis of their RdRp protein sequences.

Genetic characterization of three Cuban Trichomonas vaginalis virus. Phylogeny of Totiviridae family

Trichomonas vaginalis can be infected with double stranded RNA (dsRNA) viruses known as T. vaginalis virus (TVV). This viral infection may have important implications for trichomonal virulence and disease pathogenesis. In this study we identified and genetic characterized three strains of TVVs isolated from T. vaginalis in Cuba. The three new predicted sequences of capsid protein and RNA-dependent RNA polymerase amounted to the previously determined 20 TVV sequences and other 21 viruses of Totiviridae family were used for a phylogenetic analysis. Four distinct monophyletic clades are shown in a phylogenetic tree. One corresponds with TVVs, other with Victorivirus, Leishmaniavirus and Eimeria brunetti virus and, other with viruses of the genus Totivirus and the last with Giardiavirus. The E. brunetti virus is identified in the phylogenetic tree as independent taxon between Leishmaniavirus and Victorivirus isolates, most closely related to Victorivirus. TVV constitute a monophyletic cluster distinguishable from all other viruses in Totiviridae family. This result suggested that TVV may be grouped in a separated genus and not inside of Giardiavirus. TVVs appear to be more closely related to protozoan viruses in the genus Leishmaniavirus and to fungal viruses in the genus Victorivirus than to other protozoan and fungal viruses in Giardiavirus and Totivirus. Among TVVs, four main groups can be recognized within Trichomonasvirus cluster, which correspond with the previous species classification proposed. Further studies, with more TVV strains, especially TVV3 and 4 strains, are needed in order to determine the phylogenetic relationship among Trichomonasvirus genus and specifically if TVV2 and 3 each also constitute a well-delimited group.

Identification and molecular characterization of a new nonsegmented double-stranded RNA virus isolated from Culex mosquitoes in Japan

Two infectious agents were isolated from Culex species mosquitoes in Japan and were identified as distinct strains of a new RNA virus by a method for sequence-independent amplification of viral nucleic acids. The virus designated Omono River virus (OMRV) replicated in mosquito cells in which it produced a severe cytopathic effect. Icosahedral virus particles of approximately 40 nm in diameter were detected in the cytoplasm of infected cells. The OMRV genome was observed to consist of a nonsegmented, 7.6-kb double-stranded RNA (dsRNA) and contain two overlapping open reading frames (ORFs), namely ORF1 and ORF2. ORF1 was found to encode a putative dsRNA-binding protein, a major capsid protein, and other putative proteins, which might be generated by co- and/or post-translational processing of the ORF1 polyprotein precursor, and ORF2 was found to encode a putative RNA-dependent RNA polymerase (RdRp), which could be translated as a fusion with the ORF1 product by a -1 ribosomal frameshift. Phylogenetic analysis based on RdRp revealed that OMRV is closely related to penaeid shrimp infectious myonecrosis virus and Drosophila totivirus, which are tentatively assigned to the family Totiviridae. These results indicated that OMRV is a new member of the family of nonsegmented dsRNA viruses infecting arthropod hosts, but not fungal or protozoan hosts.

Significantly low level of small RNA accumulation derived from an encapsidated mycovirus with dsRNA genome

The role of RNA silencing as an antiviral defence has been well elucidated in plants and invertebrates, but not in filamentous fungi. We have previously determined the complete genome sequence of Magnaporthe oryzae virus 2 (MoV2), a dsRNA virus that infects the rice blast fungus Magnaporthe oryzae. In this study, we detected small interfering RNAs (siRNAs) from both positive- and negative-strand MoV2 viral RNA, suggesting that the RNA silencing machinery in M. oryzae functions against the mycovirus. Cloning and characterisation of MoV2 siRNAs indicated that, in MoV2, the ratio of virus-derived siRNAs to total small RNA is significantly lower than that in either plant viruses or Cryphonectria hypovirus 1 (CHV1), another mycovirus. Nevertheless, any MoV2-encoded proteins did not exhibit RNA silencing suppressor activity in both the plant and fungal systems. Our study suggests the existence of a novel viral strategy employed to evade host RNA silencing.

Viruses of plant pathogenic fungi

Mycoviruses are widespread in all major groups of plant pathogenic fungi. They are transmitted intracellularly during cell division, sporogenesis, and cell fusion, but apparently lack an extracellular route for infection. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups. Recent advances, however, allowed the establishment of experimental host ranges for a few mycoviruses. Although the majority of known mycoviruses have dsRNA genomes that are packaged in isometric particles, an increasing number of usually unencapsidated mycoviruses with positive-strand RNA genomes have been reported. We discuss selected mycoviruses that cause debilitating diseases and/or reduce the virulence of their phytopathogenic fungal hosts. Such fungal-virus systems are valuable for the development of novel biocontol strategies and for gaining an insight into the molecular basis of fungal virulence. The availability of viral and host genome sequences and of transformation and transfection protocols for some plant pathogenic fungi will contribute to progress in fungal virology.