Optimized approaches for the sequence determination of double-stranded RNA templates

A mitovirus related to plant mitochondrial gene confers hypovirulence on the phytopathogenic fungus Sclerotinia sclerotiorum

A double-stranded RNA (dsRNA) segment was isolated from a hypovirulent strain, HC025, of Sclerotinia sclerotiorum. The complete nucleotide sequence of the dsRNA was determined to be 2530 bp in length. Using the fungal mitochondrial genetic code, the positive strand of the dsRNA was found to contain a single large open reading frame (ORF) with the characteristic conserved motifs of the RNA-dependent RNA polymerase (RdRp). BLAST analysis revealed that RdRp shares 74% sequence identity with Sclerotinia sclerotiorum mitovirus 1 (SsMV1/KL-1). The positive strand of the dsRNA could be folded into potentially stable stem-loop structures at both the 5' and 3' terminal sequences. Moreover, the 5' and 3' terminal sequences were inverted complementary sequences and formed a panhandle structure. These results reveal that this dsRNA segment represents the replicative form of a mitovirus that is a strain of SsMV1 from the genus Mitovirus in the family Narnaviridae and was tentatively designated as Sclerotinia sclerotiorum mitovirus 1 (SsMV1/HC025). Sequence comparison and phylogenetic analysis suggest that mitovirus RdRp gene was evolutionarily related to plant mitochondrial genome. Our results demonstrate that SsMV1/HC025 infection exerted obvious effects on host biological properties. Hypovirulence feature and SsMV1/HC025 could be co-transmitted from hypovirulent strains to other virulent strains via hyphal contact. Thus, SsMV1/HC025 related to plant mitochondrial gene confers hypovirulence on S. sclerotiorum.

Molecular characterisation of an endornavirus from Rhizoctonia solani AG-3PT infecting potato

Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) is a soil-borne plant pathogenic fungus that has a broad host range, including potato. In this study, the double-stranded RNA (dsRNA) profiles were defined for 39 Rhizoctonia solani isolates representative of two different anastomosis groups (AGs) associated with black scurf of potato in New Zealand. A large dsRNA of c. 12 kb-18 kb was detected in each of the isolates, regardless of AG or virulence on potato. Characterisation of the large dsRNA from R. solani AG-3PT isolate RS002, using random amplification of total dsRNA and analyses of overlapping cDNA sequences, resulted in the assembly of a consensus sequence of 14 694 nt. A single, large open reading frame was identified on the positive strand of the assembled sequence encoding a putative polypeptide of at least 4893 amino acids, with a predicted molecular mass of 555.6 kDa. Conserved domains within this polypeptide included those for a viral methyltransferase, a viral RNA helicase 1 and an RNA-dependent RNA polymerase. The domains and their sequential organisation revealed the polyprotein was very similar to those encoded by dsRNA viruses of the genus Endornavirus, in the family Endornaviridae. This is the first report of an endornavirus in R. solani, and thus the putative virus is herein named Rhizoctonia solani endornavirus - RS002 (RsEV-RS002). Partial characterisation of the large dsRNAs in five additional AG-3PT isolates of R. solani also identified them as probable endornaviruses, suggesting this family of viruses is widespread in R. solani infecting potato. The ubiquitous nature of endornaviruses in this plant pathogen implies they may have an important, but yet uncharacterised, role in R. solani.

A novel mycovirus closely related to viruses in the genus Alphapartitivirus confers hypovirulence in the phytopathogenic fungus Rhizoctonia solani

We report here the biological and molecular attributes of a novel dsRNA mycovirus designated Rhizoctonia solani partitivirus 2 (RsPV2) from strain GD-11 of R. solani AG-1 IA, the causal agent of rice sheath blight. The RsPV2 genome comprises two dsRNAs, each possessing a single ORF. Phylogenetic analyses indicated that this novel virus species RsPV2 showed a high sequence identity with the members of genus Alphapartitivirus in the family Partitiviridae, and formed a distinct clade distantly related to the other genera of Partitiviridae. Introduction of purified RsPV2 virus particles into protoplasts of a virus-free virulent strain GD-118 of R. solani AG-1 IA resulted in a derivative isogenic strain GD-118T with reduced mycelial growth and hypovirulence to rice leaves. Taken together, it is concluded that RsPV2 is a novel dsRNA virus belonging to Alphapartitivirus, with potential role in biological control of R. solani.

Complete genome sequence of a novel hypovirus infecting Phomopsis longicolla

The complete nucleotide sequence and genome organization of a hypovirus from the isolate ME711 of Phomopsis longicolla was determined and compared to sequences of members of the family Hypoviridae. The genome of the hypovirus, tentatively named Phomopsis longicolla hypovirus 1 (PlHV1-ME711), was determined to be 9760 nucleotides long, excluding the 3' poly (A) tail. The genome contains a single large open reading frame (ORF) encoding a polyprotein designated as P307. Its genomic organization is typical of members of the proposed genus Betahypovirus (Yaegashi et al. in Virus Res 165:143-50, 2012).

Two novel mitoviruses from a Canadian isolate of the Dutch elm pathogen Ophiostoma novo-ulmi (93-1224)

Background

Ophiostoma novo-ulmi is the causative agent of Dutch elm disease (DED). It is an ascomycetous filamentous fungus that ranks as the third most devastating fungal pathogen in Canada. The disease front has spread eastward and westward from the epicentre in Ontario and Quebec and is threatening elm populations across the country. Numerous mitigation strategies have been tried to eradicate this pathogen, but success has thus far been limited. An alternative approach might utilize double-stranded RNA (dsRNA) mycoviruses which have been reported to induce hypovirulence in other fungi.

Methods

Using a modified single primer amplification technique (SPAT) in combination with chromosomal walking, we have determined the genome sequence of two RdRp encoding dsRNA viruses from an O. novo-ulmi isolate (93–1224) collected from the disease front in Winnipeg.

Results

We propose that these viruses, which we have named OnuMV1c and OnuMV7 based on sequence similarity to other Ophiostoma mitoviruses, are two new members of the genus Mitovirus in the family Narnaviridae.

Conclusions

The discovery of such dsRNA elements raises the potential for engineering these viruses to include other genetic elements, such as anti-sense or interfering RNAs, to create novel and highly specific biological controls. Naïve fungal hosts could be infected with both the engineered molecule and a helper mitovirus encoding an RdRp which would provide replication capacity for both molecules.

A novel mycovirus from Clitocybe odora

The Ninth Report of the International Committee on Taxonomy of Viruses (ICTV) reports only a few species whose members replicate in fungi. Most of these mycoviruses are described to replicate in phytopathogenic and commercially cultivated fungi. A few reports describe virus-like symptoms and virus-like particles in non-cultivated basidiocarps such as Boletus edulis, Laccaria spp. and Cantharellus spp. However, viral sequences from non-cultivated Agaricomycotina are not available yet. In this report, I present a partial sequence of a virus found in Clitocybe odora (Bull.:Fr.) P. Kumm var. odora coding for a putative RNA-dependent RNA polymerase (RdRp) and a small 20-kDa ORF that may encode a coat protein (CP). The sequence of the putative RdRp (ORF 1) of C. odora clusters with those of the Tanathephorus cucumeris virus RdRp and the Tuber aestivum mitovirus RdRp. In addition to sequence homology, Tanathephorus cucumeris virus shows a similar codon usage and TA content in the 5'- and 3' non-translated regions, but it does not encode a putative CP. A viral DNA form proposed for Tanathephorus cucumeris virus was not found in Clitocybe odora. This viral sequence does not fit into any of the existing virus taxa.

The complete sequence of tobacco mosaic virus isolate Ohio V reveals a high accumulation of silent mutations in all open reading frames

TMVOhioV was first described 1969 by [1] because it did break resistance of tomato breeding lines containing Tm-1- and Tm-2 resistance genes. It was obtained 1987 from Wetter (Saarbrücken, Germany) and transferred into the DSMZ-Plant Virus Collection (Braunschweig, Germany). A partial sequence of TMVOhioV, the CP gene, has been reported [11] and its comparison with a TMV type isolates (TMVtype), e.g. EMBL: V01409, revealed 50 point mutations in a total of 477 nucleotides (nts) leading to the replacement of only 7 amino acids (aa). In order to investigate the mutations in the non-translated regions and the number of silent mutation in the three other open reading frames (ORF), we sequenced the complete genome of isolate TMVOhioV and compared it to those of other Tobamoviruses.

A novel mycovirus closely related to hypoviruses that infects the plant pathogenic fungus Sclerotinia sclerotiorum

Three dsRNA segments, two similarly sized at 9.5kbp and a third one of approximately 3.6kbp, were extracted from a hypovirulent strain SZ-150 of Sclerotinia sclerotiorum. The complete cDNA sequence of one of the two large dsRNA segment (10398bp, excluding the poly (A) tail) reveals a single ORF that encodes a polyprotein with conserved domains of putative papain-like protease, UDP glucose/sterol glycosyltransferase, RNA-dependent RNA polymerase and viral RNA Helicase. This virus is closely related to Cryphonectria hypovirus (CHV) 3/GH2 and CHV4/SR2 in the family Hypoviridae and designated as Sclerotinia sclerotiorum hypovirus 1 (SsHV1/SZ-150). The satellite-like 3.6kbp dsRNA segment (S-dsRNA) shares high sequence identity with the 5'-UTR of SsHV1/SZ-150. SsHV1/SZ-150 alone is not the primary causal agent for hypovirulence of strain SZ-150 since strains without the S-dsRNA show normal phenotype. This is the first report of a naturally occurring hypovirus that infects a fungus other than Cryphonectria parasitica.

Rapid isolation of mycoviral double-stranded RNA from Botrytis cinerea and Saccharomyces cerevisiae

BACKGROUND

In most of the infected fungi, the mycoviruses are latent or cryptic, the infected fungus does not show disease symptoms, and it is phenotypically identical to a non-infected strain of the same species. Because of these properties, the initial stage in the search for fungi infected with mycoviruses is the detection of their viral genome, which in most of the described cases corresponds to double-stranded RNA (dsRNA). So to analyze a large number of fungal isolates it is necessary to have a simple and rapid method to detect dsRNA.

RESULTS

A rapid method to isolate dsRNA from a virus-infected filamentous fungus, Botrytis cinerea, and from a killer strain of Saccharomyces cerevisiae using commercial minicolumns packed with CF11 cellulose was developed. In addition to being a rapid method, it allows to use small quantities of yeasts or mycelium as starting material, being obtained sufficient dsRNA quantity that can later be analyzed by agarose gel electrophoresis, treated with enzymes for its partial characterization, amplified by RT-PCR and cloned in appropriate vectors for further sequencing.

CONCLUSIONS

The method yields high quality dsRNA, free from DNA and ssRNA. The use of nucleases to degrade the DNA or the ssRNA is not required, and it can be used to isolate dsRNA from any type of fungi or any biological sample that contains dsRNA.