Molecular characterization of a novel fusarivirus infecting the plant-pathogenic fungus Alternaria solani.

A novel mycovirus belonging to the proposed family "Fusariviridae" was discovered in Alternaria solani by sequencing a cDNA corresponding to double-stranded RNA extracted from this phytopathogenic fungus. The virus was tentatively named "Alternaria solani fusarivirus 1" (AsFV1). AsFV1 has a single-stranded positive-sense (+ssRNA) genome of 6845 nucleotides containing three open reading frames (ORFs) and a poly(A) tail. The largest ORF, ORF1, encodes a large polypeptide of 1,556 amino acids (aa) with conserved RNA-dependent RNA polymerase and helicase domains. The ORF2 and ORF3 have overlapping regions, encoding a putative protein of 522 amino acids (aa) and a putative protein of 105 amino acids (aa), respectively, both of unknown function. A multiple sequence alignment and phylogenetic analysis revealed that AsFV1 could be a new member of the "Fusariviridae". This is the first report of the full-length nucleotide sequence of a fusarivirus that infects Alternaria solani.

Full genome sequence of a new three-segment gammapartitivirus from the phytopathogenic fungus Alternaria tenuissima on cotton in China.

In this study, a new double-stranded RNA (dsRNA) virus, Alternaria tenuissima partitivirus 1 (AttPV1), was isolated from Alternaria tenuissima strain XJ-BZ-2-6, a phytopathogenic fungus infecting cotton in China. The genome of AttPV1 comprised three dsRNAs of 1,785 nt (dsRNA1), 1,545 nt (dsRNA2), and 1,537 nt (dsRNA3) in length, the nucleotide sequence of which was determined using reverse transcription polymerase chain reaction, random-primed clones, and RNA-ligase-mediated rapid amplification of cDNA ends. dsRNA1 had a single open reading frame encoding a putative 61.54-kDa RNA-dependent RNA polymerase (RdRp). dsRNA2 and dsRNA3 were predicted to encode putative coat proteins (CPs) of 47.90 kDa and 46.25 kDa, respectively. The RdRp domain shared 63.54-73.17% amino acid sequence identity with members of the genus Gammapartitivirus. Phylogenetic trees based on RdRp or CP sequences showed that AttPV1 clustered with members of the genus Gammapartitivirus. Hence, these results indicate that AttPV1 is a new gammapartitivirus from A. tenuissima.

A novel mycovirus isolated from the plant-pathogenic fungus Alternaria dianthicola.

Here, we describe the molecular characterization of a novel mycovirus isolated from a phytopathogenic fungus, Alternaria dianthicola, which we have named "Alternaria dianthicola dsRNA virus 1" (AdRV1). AdRV1 has a genome of 3,014 bp that contains two non-overlapping open reading frames (ORF1 and 2) coding for a hypothetical protein and an RNA-dependent RNA polymerase (RdRp), respectively. Based on the RdRp, AdRV1 is phylogenetically related to some unclassified dsRNA mycoviruses, including Alternaria longipes dsRNA virus 1, and shows a distant relationship to members of the family Partitiviridae. To the best of our knowledge, this is the first report of mycovirus infecting A. dianthicola.

Molecular and biological characterization of a novel strain of Alternaria alternata chrysovirus 1 identified from the pathogen Alternaria tenuissima causing watermelon leaf blight.

The leaf blight caused by the genus Alternaria is one of the most epidemic diseases on watermelon, and A. tenuissima is the dominant pathogenic species in China. Mycoviruses are found ubiquitously in filamentous fungi, and an increasing number of novel mycoviruses infecting the genus Alternaria have been reported. In this study, a mycovirus from A. tenuissima strain SD-BZF-12 was identified and characterized, whose genome size was very similar with Alternaria alternata chrysovirus 1-N18 (AaCV1-N18). The dsRNA1- and dsRNA2-encoded proteins of the virus had 99 % identities with counterparts of AaCV1-N18; and the dsRNA3- and dsRNA4-encoded proteins of the virus showed the 80 % and 94 % sequence identities with proteins deduced from dsRNA4 and dsRNA3 of AaCV1-N18, respectively. Intriguingly, dsRNA5 of the virus encoded a truncated protein with 68 amino acids (aa) by comparing with 115 aa of AaCV1-N18 dsRNA5. Phylogenetic analysis of RNA-dependent RNA polymerase domain suggested that the virus clustered together with AaCV1-N18. Based on these characteristics, the mycovirus was identified to be a novel strain of AaCV1 and designated as AaCV1-AT1. In addition, no obvious differences were observed on colony morphology between AaCV1-AT1-infected and virus-cured strains of A. tenuissima; however, AaCV1-AT1 infection reduced colony growth rate and spore production ability on host fungus, and increased the median effective concentration of difenoconazole or tebuconazole on its host. This is the first report of AaCV1-AT1 associated with A. tenuissima.

Novel Victorivirus from a Pakistani Isolate of Alternaria alternata Lacking a Typical Translational Stop/Restart Sequence Signature.

The family Totiviridae currently contains five genera Totivirus, Victorivirus, Leishmavirus, Trichomonasvirus, and Giardiavirus. Members in this family generally have a set of two-open reading frame (ORF) elements in their genome with the 5'-proximal ORF (ORF1) encoding a capsid protein (CP) and the 3'-proximal one (ORF2) for RNA-dependent RNA polymerase (RdRp). How the downstream open reading frames (ORFs) are expressed is genus-specific. All victoriviruses characterized thus far appear to use the stop/restart translation mechanism, allowing for the expression of two separate protein products from bicitronic genome-sized viral mRNA, while the totiviruses use a -1 ribosomal frame-shifting that leads to a fusion product of CP and RdRp. We report the biological and molecular characterization of a novel victorivirus termed Alternaria alternata victorivirus 1 (AalVV1) isolated from Alternaria alternata in Pakistan. The phylogenetic and molecular analyses showed AalVV1 to be distinct from previously reported victoriviruses. AalVV1 appears to have a sequence signature required for the -1 frame-shifting at the ORF1/2 junction region, rather than a stop/restart key mediator. By contrast, SDS-polyacrylamide gel electrophoresis and peptide mass fingerprinting analyses of purified virion preparations suggested the expression of two protein products, not a CP-RdRp fusion product. How these proteins are expressed is discussed in this study. Possible effects of infection by this virus were tested in two fungal species: A. alternata and RNA silencing proficient and deficient strains of Cryphonectria parasitica, a model filamentous fungus. AalVV1 showed symptomless infection in all of these fungal strains, even in the RNA silencing deficient C. parasitica strain.

Complete genome sequence of a new botybirnavirus isolated from a phytopathogenic Alternaria alternata in China.

A new double-stranded RNA (dsRNA) virus named Alternaria alternata botybirnavirus 1 (AaBRV1) was isolated from Alternaria alternata strain SD-BZF-19, a phytopathogenic fungus infecting watermelon in China. The genome of AaBRV1 consists of two dsRNA segments (dsRNAs 1 and 2), 6,130 and 5,862 bp in size, respectively. The sequence contains two putative open reading frames (ORFs) which encode two polyproteins of 1,874 and 1,784 amino acids, respectively. Nucleotide sequence comparisons revealed that the two ORFs of AaBRV1 have the highest similarity 60.3% and 56.7%, respectively, with dsRNAs 1 and 2 of Botrytis porri RNA virus 1 (BpRV1). The two polyproteins encoded by dsRNA1 and dsRNA2 shared the highest amino acid identities with the cap-pol fusion protein (60.2%) and hypothetical protein (53.7%) of BpRV1, respectively. AaBRV1 is composed of isometric particles, approximately 35 nm in diameter. Phylogenetic analysis of the RNA dependent RNA polymerase (RdRp) domain of the polyprotein revealed that AaBRV1 clusters together with members of the genus Botybirnavirus. These findings support the discovery of a new botybirnavirus in A. alternata.

Molecular and biological characterization of a novel botybirnavirus identified from a Pakistani isolate of Alternaria alternata.

Mycoviruses ubiquitously infect a wide range of fungal hosts in the world. The current study reports a novel double stranded RNA (dsRNA) virus, termed Alternaria alternata botybirnavirus 1 (AaBbV1), infecting a Pakistani strain, 4a, of a phytopathogenic ascomycetous fungus Alternaria alternata. A combined approach of next generation and conventional terminal end sequencing of the viral genome revealed that the virus is a distinct member of the genus Botybirnavirus. This virus comprised of two segments (dsRNA1 and dsRNA2) of sizes 6127 bp and 5860 bp respectively. The dsRNA1-encoded protein carrying the RNA-dependent RNA polymerase domain showed 61% identity to the counterpart of Botrytis porri botybirnavirus 1 and lower levels of amino acid similarity with those of other putative botybirnaviruses and the fungal dsRNA viruses such as members of the families Totiviridae, Chrysoviridae and Megabirnaviridae. The dsRNA2-encoded protein showed resemblance with corresponding proteins of botybirnaviruses. Electron microscopy showed AaBbV1 to form spherical particles of 40 nm in diameter. Biochemical analyses showed that two structural proteins encoded by dsRNA1 and dsRNA2 underwent processing to some extent during particle purification, resulting in the appearance of multiple smaller products. Phylogenetic analyses of structural proteins suggested that their coding region might have been duplicated once and maintained without recombination. Protoplast fusion technique allowed for the introduction of AaBbV1 into a virus free Japanese strain of A. alternata and demonstrated its symptomless infection by the virus. Interesting similarities and dissimilarities between AaBbV1 and other previously reported botybirnaviruses are also discussed.

Molecular characterization of a novel mycovirus in Alternaria alternata manifesting two-sided effects: Down-regulation of host growth and up-regulation of host plant pathogenicity.

A double-stranded RNA (dsRNA) mycovirus was detected in a strain of Alternaria alternata showing impaired growth phenotypes. The A. alternata strain is the Japanese pear pathotype, which produces a host-specific AK-toxin. Sequence analysis of the viral genome dsRNAs revealed that this mycovirus consists of five dsRNAs and is evolutionarily related to members of the family Chrysoviridae; the virus was named Alternaria alternata chrysovirus 1 (AaCV1). AaCV1-ORF2 protein accumulated in dsRNA-high-titer sub-isolates with severely impaired phenotypes; heterologous AaCV1-ORF2 overexpression in Saccharomyces cerevisiae caused growth inhibition. In contrast to this yeast growth inhibition phenomenon, the dsRNA-high-titer isolates displayed enhanced pathogenicity against Japanese pear plants, in accordance with a 13-fold increase in AK-toxin level in one such isolate. These findings indicated that AaCV1 is a novel mycovirus that exhibits two contrasting effects, impairing growth of the host fungus while rendering the host 'hypervirulent' to the plant.

A novel mycovirus associated to Alternaria alternata comprises a distinct lineage in Partitiviridae.

In the present work, we report a novel mycovirus that infects Alternaria alternata. The mycovirus has isometric particles of approximately 30nm and the genome consists of two molecules of dsRNA, dsRNA1 with 1833bp, encoding a putative RNA-dependent RNA polymerase (RdRp) and dsRNA2, with 1680bp in length, encoding the putative capsid protein (CP). RdRp analysis revealed low amino acid identity with RdRps with species in the genus Gammapartitivirus, and the alignment of the RdRp revealed all the six conserved motifs present in members of Partitiviridae. The putative coat protein (CP) analysis revealed similarity with the putative CP of Botryosphaeria dothidea partitivirus 1 (BdPV1), a divergent partitivirus. We propose that Alternaria alternata partitivirus 1 (AtPV1) is a novel species and comprises a distinct lineage related to genus Gammapartitivirus in the family Partitiviridae, apparently on the threshold of radiation of a new genus, together with BdPV1. Vertical transmission tests showed that AtPV1 was transmitted to 100% conidial progeny and standard curing was unable to eliminate it from the host, characterizing it as a persistent virus. The absence of a virus-free isogenic lineage prevented us from accessing the details of the interaction between AtPV1 and A. alternata. Therefore, it remains unclear whether the morphological plasticity observed or the inability of the A. alternata isolate AVi1 to cause disease in plants is associated with AtPV1 infection.

Characterization of a novel botybirnavirus isolated from a phytopathogenic Alternaria fungus.

Alternaria fungi are important pathogens infecting a wide variety of organisms. Here, we report a novel double-stranded RNA (dsRNA) mycovirus named Alternaria botybirnavirus 1 (ABRV1) isolated from a phytopathogenic Alternaria sp. strain (SCFS-3) infecting a pear tree in China. ABRV1 has two dsRNA components (dsRNAs 1 and 2) with the sizes of 6,188 and 5,903 bp, containing two putative open reading frames encoding two polyproteins (202 and 192 kDa, respectively). The polyprotein encoded by ABRV1 dsRNA1 shares 41% amino acid (aa) sequence identity with the one encoded by dsRNA2 (instead of dsRNA1) of Sclerotinia sclerotiorum botybirnavirus 1 (SsBRV1). Conversely, the polyprotein encoded by ABRV1 dsRNA2 shares 46% aa sequence identity with the one (i.e., cap-pol fusion protein) encoded by SsBRV1 dsRNA1. ABRV1 has isometric spherical virus particles (~40 nm in diameter), putatively composed of the 60-, 70- and 80-kDa structural proteins. The genomic organization and phylogenetic analyses revealed that ABRV1 belongs to a newly proposed family "Botybirnaviridae", and to our knowledge, this is the first report of a botybirnavirus infecting an Alternaria sp. strain.

A mitovirus isolated from the phytopathogenic fungus Alternaria brassicicola.

Alternaria brassicicola is one of the causal agents of alternaria blackspot in rapeseed. In this study, a dsRNA segment was isolated and sequenced from the fungus. The complete nucleotide sequence of the dsRNA was 2506 bp in length and, using the fungal mitochondrial genetic code, was predicted to contain a single large open reading frame (ORF) in the positive strand. This ORF was predicted to encode a protein with 719 amino acids that contains characteristic conserved motifs of the RNA-dependent RNA polymerase (RdRp). BLAST analysis revealed that this protein had significant sequence similarity to the RdRp from viruses of the genus Mitovirus. These results indicated that the dsRNA segment represents the replicative form of a mitovirus, which is tentatively designated "Alternaria brassicicola mitovirus 1" (AbMV1) and is a new member of the genus Mitovirus in the family Narnaviridae.

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

The phytopathogenic fungus Alternaria spp. contains a variety of double-stranded RNA (dsRNA) elements of different sizes. Detailed analysis of next-generation sequencing data obtained using dsRNA purified from Alternaria arborescens, from which we had previously found Alternaria arborescens victorivirus 1, revealed the presence of another mycoviral-like dsRNA of approximately 2.5 kbp in length. When using the fungal mitochondrial genetic code, this dsRNA has a single open reading frame that potentially encodes an RNA-dependent RNA polymerase (RdRp) with significant to sequence similarity to those of viruses of the genus Mitovirus. Moreover, both the 5'- and 3'-untranslated regions have the potential to fold into stable stem-loop structures, which is characteristic of mitoviruses. Pairwise comparisons and phylogenetic analysis of the deduced amino acid sequences of RdRp indicated that the virus we identified in A. arborescens is a distinct member of the genus Mitovirus in the family Narnaviridae, designated as "Alternaria arborescens mitovirus 1" (AaMV1).

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.

Characterization of a novel single-stranded RNA virus, closely related to fusariviruses, infecting the plant pathogenic fungus Alternaria brassicicola.

The alternaria blackspot of rapeseed is one of the most prominent diseases of rapeseed. It is caused by three species of the genus Alternaria: Alternaria brassicicola, Alternaria brassicae, and Alternaria raphanin. Here we report a novel positive-sense RNA virus from an A. brassicicola strain 817-14. The virus has a 6639 nucleotide (nt) long genome, excluding a poly (A)-tail, and was predicted to contain three putative open reading frames (ORF1, ORF2, and ORF3). The large ORF1 encoded a 174-kDa polyprotein (composed of 1522 amino acid residues) containing a conserved RNA-dependent RNA polymerase (RdRp) domain and a helicase domain. The other two smaller ORFs encoded polypeptides with unknown function. Homology search and phylogenetic analysis, based on the RdRp and helicase domains, suggest that this virus is related to and grouped with Sclerotinia sclerotiorum fusarivirus 1 (SsFV1), Rosellinia necatrix fusarivirus 1 (RnFV1), Fusarium graminearum virus-DK21 (FgV1), and Penicillium roqueforti RNA mycovirus 1 (PrRV1), all of which belong to a newly proposed family Fusariviridae. For this study, we designed the virus as "Alternaria brassicicola fusarivirus 1" (AbFV1). Virus elimination revealed that AbFV1 has no conspicuous impact on the biological properties of its host.

Genome sequence of a novel endornavirus from the phytopathogenic fungus Alternaria brassicicola.

In an effort to discover new mycoviruses from phytopathogenic fungi, a dsRNA molecule of 10,290 nt, resembling those associated with the viruses belonging to the family Endornaviridae, was isolated from Alternaria brassicicola, one of the causal agents of rapeseed black spot disease. Genome analysis revealed the presence of a single open reading frame coding for a polyprotein of 3400 aa containing conserved viral methyltransferase (MTR), viral RNA helicase 1 (Hel-1), and RNA-dependent RNA polymerase (RdRp) domains. In addition, a cysteine-rich region (CRR) with conserved CXCC motifs, shared among several endornaviruses, was also identified between the MTR and Hel-1 domains. Phylogenetic analysis based on the RdRp sequence strongly suggested that the virus infecting A. brassicicola should be considered a representative of a novel endornavirus species, and this virus was designated as Alternaria brassicicola endornavirus 1 (AbEV1).

The complete genome sequence of a novel mycovirus from Alternaria longipes strain HN28.

The complete nucleotide sequence of Alternaria longipes dsRNA virus 1 (AlRV1), a novel double-stranded RNA (dsRNA) mycovirus, was determined and analyzed. AlRV1-HN28 contains a single dsRNA genome segment 3415 base pairs in length (excluding the 3' poly(A) tail) and was predicted to contain two discontiguous open reading frames (ORFs, ORF A and ORF B). The 5'-proximal ORF A (1182 nt) potentially encodes a protein of 394 amino acids (aa) with a predicted molecular mass of 43 kDa; this protein showed no significant similarities to any other sequences in any of the NCBI protein databases. The 3'-proximal ORF B (1737 nt) encodes a protein of 579 aa with a predicted molecular mass of 65 kDa; this protein sequence shares similarities with the conserved domains of RNA-dependent RNA polymerases of other mycoviruses. Phylogenetic analysis indicated that AlRV1-HN28 was closely related to four other unclassified viruses, which suggests that the AlRV1-HN28 isolated from Alternaria longipes may belong to a new family of dsRNA mycoviruses. This is the first report of the full-length nucleotide sequence of a mycovirus that infects Alternaria longipes.

A novel mycovirus associated with four double-stranded RNAs affects host fungal growth in Alternaria alternata.

Four double-stranded RNAs (dsRNAs), referred to as dsRNA 1 (3617 bp), dsRNA 2 (2794 bp), dsRNA 3 (2576 bp) and dsRNA 4 (1420 bp), were detected in the EGS 35-193 strain of Alternaria alternata at high concentration ( approximately 3 microg/g dried mycelium). This strain had an impaired growth phenotype. By exposing the strain to cycloheximide during hyphal tip isolation, we isolated strains which had normal mycelial growth and pigmentation, in which decreased levels of the dsRNAs were observed ( approximately 0.3 microg/g dried mycelium). These results indicate that this dsRNA mycovirus might be involved in modulating traits of its fungal host, A. alternata. The buoyant density of isometric virus particles (about 33 nm in diameter) containing these dsRNAs in CsCl was 1.35-1.40 g/cm(3) depending on the size of the packaged dsRNAs. The dsRNA 1 encodes a single open reading frame (3447 nt) containing the conserved motifs of viral RNA-dependent RNA polymerase (RdRp), which is related to the ORF encoded by dsRNA 1 of Aspergillus mycovirus 341. It is noteworthy that all of the coding strands of the four dsRNA genomes have 3'-poly (A) tails ranging from 33 to 50 nt in length. We named this novel dsRNA mycovirus in the EGS 35-193 strain A. alternata virus-1 (AaV-1).