The Experts below are selected from a list of 54 Experts worldwide ranked by ideXlab platform
Leslie L. Domier - One of the best experts on this subject based on the ideXlab platform.
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Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens
Journal of virology, 2016Co-Authors: Shin-yi Lee Marzano, Carl A. Bradley, Berlin D. Nelson, Olutoyosi O Ajayi-oyetunde, Teresa J. Hughes, Glen L. Hartman, Darin M. Eastburn, Leslie L. DomierAbstract:Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts. Plant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
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Reprint of "Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes".
Virus Research, 2016Co-Authors: Shin-yi Lee Marzano, Leslie L. DomierAbstract:Abstract Mycoviruses can be beneficial to plants in that they can debilitate pathogenic fungi thereby reducing the severity of associated plant diseases. Studies to date have focused primarily on culturable fungi that represent a fraction of natural fungal populations. The nonculturable fungi, however, can harbor diverse populations of mycoviruses that reduce plant disease or enhance resistance to abiotic stress. Metatranscriptome analysis of field-grown plant samples using high-throughput sequencing offers the possibility of unbiased detection and quantification of mycoviruses regardless of the culturability of their fungal hosts together with the complete associated microbial consortia. In this study, we describe the fungal viromes of the phyllosphere of production soybean fields in Illinois, USA by analyzing the metatranscriptomes of thousands of soybean leaf samples collected during the 2008 and 2009 growing seasons. The analyses identified 25 partial genome sequences that represented at least 22 mycovirus genomes, only one of which had been described previously. The novel mycovirus genomes showed similarity to 10 distinct lineages including the genera Alphapartitivirus , Botybirnavirus, Endornavirus , Mitovirus , Mycoflexivirus , Ourmiavirus , Totivirus , Victorivirus , family Tombusviridae , order Mononegavirales , and the recently proposed genus Gemycircularvirus. The present study adds to the wealth of mycoviruses associated with plant phytobiomes and establishes groundwork needed for further characterization of the viruses.
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Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes
Virus Research, 2015Co-Authors: Shin-yi Lee Marzano, Leslie L. DomierAbstract:Mycoviruses can be beneficial to plants in that they can debilitate pathogenic fungi thereby reducing the severity of associated plant diseases. Studies to date have focused primarily on culturable fungi that represent a fraction of natural fungal populations. The nonculturable fungi, however, can harbor diverse populations of mycoviruses that reduce plant disease or enhance resistance to abiotic stress. Metatranscriptome analysis of field-grown plant samples using high-throughput sequencing offers the possibility of unbiased detection and quantification of mycoviruses regardless of the culturability of their fungal hosts together with the complete associated microbial consortia. In this study, we describe the fungal viromes of the phyllosphere of production soybean fields in Illinois, USA by analyzing the metatranscriptomes of thousands of soybean leaf samples collected during the 2008 and 2009 growing seasons. The analyses identified 25 partial genome sequences that represented at least 22 mycovirus genomes, only one of which had been described previously. The novel mycovirus genomes showed similarity to 10 distinct lineages including the genera Alphapartitivirus, Botybirnavirus, Endornavirus, Mitovirus, Mycoflexivirus, Ourmiavirus, Totivirus, Victorivirus, family Tombusviridae, order Mononegavirales, and the recently proposed genus Gemycircularvirus. The present study adds to the wealth of mycoviruses associated with plant phytobiomes and establishes groundwork needed for further characterization of the viruses.
Shin-yi Lee Marzano - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Botourmiaviridae.
The Journal of general virology, 2020Co-Authors: Michael Arribas Ayllon, Shin-yi Lee Marzano, Massimo Turina, Livia Donaire, Jiatao Xie, Luca Nerva, Daohong JiangAbstract:The family Botourmiaviridae includes viruses infecting plants and filamentous fungi containing a positive-sense, ssRNA genome that can be mono- or multi-segmented. Genera in the family include: Ourmiavirus (plant viruses), and Botoulivirus, Magoulivirus and Scleroulivirus (fungal viruses). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the family Botourmiaviridae, which is available at ictv.global/report/botourmiaviridae.
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Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens
Journal of virology, 2016Co-Authors: Shin-yi Lee Marzano, Carl A. Bradley, Berlin D. Nelson, Olutoyosi O Ajayi-oyetunde, Teresa J. Hughes, Glen L. Hartman, Darin M. Eastburn, Leslie L. DomierAbstract:Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts. Plant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
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Reprint of "Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes".
Virus Research, 2016Co-Authors: Shin-yi Lee Marzano, Leslie L. DomierAbstract:Abstract Mycoviruses can be beneficial to plants in that they can debilitate pathogenic fungi thereby reducing the severity of associated plant diseases. Studies to date have focused primarily on culturable fungi that represent a fraction of natural fungal populations. The nonculturable fungi, however, can harbor diverse populations of mycoviruses that reduce plant disease or enhance resistance to abiotic stress. Metatranscriptome analysis of field-grown plant samples using high-throughput sequencing offers the possibility of unbiased detection and quantification of mycoviruses regardless of the culturability of their fungal hosts together with the complete associated microbial consortia. In this study, we describe the fungal viromes of the phyllosphere of production soybean fields in Illinois, USA by analyzing the metatranscriptomes of thousands of soybean leaf samples collected during the 2008 and 2009 growing seasons. The analyses identified 25 partial genome sequences that represented at least 22 mycovirus genomes, only one of which had been described previously. The novel mycovirus genomes showed similarity to 10 distinct lineages including the genera Alphapartitivirus , Botybirnavirus, Endornavirus , Mitovirus , Mycoflexivirus , Ourmiavirus , Totivirus , Victorivirus , family Tombusviridae , order Mononegavirales , and the recently proposed genus Gemycircularvirus. The present study adds to the wealth of mycoviruses associated with plant phytobiomes and establishes groundwork needed for further characterization of the viruses.
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Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes
Virus Research, 2015Co-Authors: Shin-yi Lee Marzano, Leslie L. DomierAbstract:Mycoviruses can be beneficial to plants in that they can debilitate pathogenic fungi thereby reducing the severity of associated plant diseases. Studies to date have focused primarily on culturable fungi that represent a fraction of natural fungal populations. The nonculturable fungi, however, can harbor diverse populations of mycoviruses that reduce plant disease or enhance resistance to abiotic stress. Metatranscriptome analysis of field-grown plant samples using high-throughput sequencing offers the possibility of unbiased detection and quantification of mycoviruses regardless of the culturability of their fungal hosts together with the complete associated microbial consortia. In this study, we describe the fungal viromes of the phyllosphere of production soybean fields in Illinois, USA by analyzing the metatranscriptomes of thousands of soybean leaf samples collected during the 2008 and 2009 growing seasons. The analyses identified 25 partial genome sequences that represented at least 22 mycovirus genomes, only one of which had been described previously. The novel mycovirus genomes showed similarity to 10 distinct lineages including the genera Alphapartitivirus, Botybirnavirus, Endornavirus, Mitovirus, Mycoflexivirus, Ourmiavirus, Totivirus, Victorivirus, family Tombusviridae, order Mononegavirales, and the recently proposed genus Gemycircularvirus. The present study adds to the wealth of mycoviruses associated with plant phytobiomes and establishes groundwork needed for further characterization of the viruses.
Massimo Turina - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Botourmiaviridae.
The Journal of general virology, 2020Co-Authors: Michael Arribas Ayllon, Shin-yi Lee Marzano, Massimo Turina, Livia Donaire, Jiatao Xie, Luca Nerva, Daohong JiangAbstract:The family Botourmiaviridae includes viruses infecting plants and filamentous fungi containing a positive-sense, ssRNA genome that can be mono- or multi-segmented. Genera in the family include: Ourmiavirus (plant viruses), and Botoulivirus, Magoulivirus and Scleroulivirus (fungal viruses). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the family Botourmiaviridae, which is available at ictv.global/report/botourmiaviridae.
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ICTV Virus Taxonomy Profile: Ourmiavirus.
Journal of General Virology, 2017Co-Authors: Massimo Turina, Mina Rastgou, Bradley I. Hillman, Keramat Izadpanah, Cristina RosaAbstract:Members of the plant virus genus Ourmiavirus are characterized by having non-enveloped bacilliform virions with a series of discrete lengths from 30 to 62 nm composed of a single coat protein (CP). The genome consists of three positive-sense single-stranded RNAs, each encoding a single protein. The RNA-dependent RNA polymerase (RdRp) has closest similarity to that of viruses from the family Narnaviridae; the movement protein (MP) is similar to the MPs of tombusviruses; the CP shows limited similarity to the CPs of several plant and animal viruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the genus Ourmiavirus, which is available at www.ictv.global/report/Ourmiavirus.
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Identification of Ourmiavirus 30K movement protein amino acid residues involved in symptomatology, viral movement, subcellular localization and tubule formation.
Molecular Plant Pathology, 2016Co-Authors: Paolo Margaria, Charles T Anderson, Massimo Turina, Cristina RosaAbstract:Several plant viruses encode movement proteins (MPs) classified in the 30K superfamily. Despite a great functional diversity, alignment analysis of MP sequences belonging to the 30K superfamily revealed the presence of a central core region, including amino acids potentially critical for MP structure and functionality. We performed alanine-scanning mutagenesis of the Ourmia melon virus (OuMV) MP, and studied the effects of amino acid substitutions on MP properties and virus infection. We identified five OuMV mutants that were impaired in systemic infection in Nicotiana benthamiana and Arabidopsis thaliana, and two mutants showing necrosis and pronounced mosaic symptoms, respectively, in N. benthamiana. Green fluorescent protein fusion constructs (GFP:MP) of movement-defective MP alleles failed to localize in distinct foci at the cell wall, whereas a GFP fusion with wild-type MP (GFP:MPwt) mainly co-localized with plasmodesmata and accumulated at the periphery of epidermal cells. The movement-defective mutants also failed to produce tubular protrusions in protoplasts isolated from infected leaves, suggesting a link between tubule formation and the ability of OuMV to move. In addition to providing data to support the importance of specific amino acids for OuMV MP functionality, we predict that these conserved residues might be critical for the correct folding and/or function of the MP of other viral species in the 30K superfamily.
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Reverse genetic analysis of Ourmiaviruses reveals the nucleolar localization of the coat protein in Nicotiana benthamiana and unusual requirements for virion formation.
Journal of Virology, 2011Co-Authors: Giulia Crivelli, Marina Ciuffo, Vera Masenga, Andrea Genre, Massimo TurinaAbstract:Ourmia melon virus (OuMV) is the type member of the genus Ourmiavirus. These viruses have a trisegmented genome, each part of which encodes a single protein. Ourmiaviruses share a distant similarity with other plant viruses only in their movement proteins (MP), whereas their RNA-dependent RNA polymerase (RdRP) shares features only with fungal viruses of the family Narnaviridae. Thus, Ourmiaviruses are in a unique phylogenetic position among existing plant viruses. Here, we developed an agroinoculation system to launch infection in Nicotiana benthamiana plants. Using different combinations of the three segments, we demonstrated that RNA1 is necessary and sufficient for cis-acting replication in the agroinfiltrated area. RNA2 and RNA3, encoding the putative movement protein and the coat protein (CP), respectively, are both necessary for successful systemic infection of N. benthamiana. The CP is dispensable for long-distance transport of the virus through vascular tissues, but its absence prevents efficient systemic infection at the exit sites. Virion formation occurred only when the CP was translated from replication-derived RNA3. Transient expression of a green fluorescent protein-MP (GFP-MP) fusion via agroinfiltration showed that the MP is present in cytoplasmic connections across plant cell walls; in protoplasts the GFP-MP fusion stimulates the formation of tubular protrusions. Expression through agroinfiltration of a GFP-CP fusion displays most of the fluorescence inside the nucleus and within the nucleolus in particular. Nuclear localization of the CP was also confirmed through Western blot analysis of purified nuclei. The significance of several unusual properties of OuMV for replication, virion assembly, and movement is discussed in relation to other positive-strand RNA viruses.
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Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin.
The Journal of general virology, 2009Co-Authors: Mina Rastgou, M K Habibi, Y I Wolf, R. G. Milne, Keramat Izadpanah, Vera Masenga, Eugene V. Koonin, Massimo TurinaAbstract:Ourmia melon virus (OuMV), Epirus cherry virus (EpCV) and Cassava virus C (CsVC) are three species placed in the genus Ourmiavirus. We cloned and sequenced their RNA genomes. The sizes of the three genomic RNAs of OuMV, the type member of the genus, were 2814, 1064 and 974 nt and each had one open reading frame. RNA1 potentially encoded a 97.5 kDa protein carrying the GDD motif typical of RNA-dependent RNA polymerases (RdRps). The putative RdRps of Ourmiaviruses are distantly related to known viral RdRps, with the closest similarity and phylogenetic affinity observed with fungal viruses of the genus Narnaviridae. RNA2 encoded a 31.6 kDa protein which, expressed in bacteria as a His-tag fusion protein and in plants through agroinfiltration, reacted specifically with antibodies made against tubular structures found in the cytoplasm. The ORF2 product is significantly similar to movement proteins of the genus Tombusviridae, and phylogenetic analysis supported this evolutionary relationship. The product of OuMV ORF3 is a 23.8 kDa protein. This protein was also expressed in bacteria and plants, and reacted specifically with antisera against the OuMV coat protein. The sequence of the ORF3 protein showed limited but significant similarity to capsid proteins of several plant and animal viruses, although phylogenetic analysis failed to reveal its most likely origin. Taken together, these results indicate that Ourmiaviruses comprise a unique group of plant viruses that might have evolved by reassortment of genomic segments of RNA viruses infecting hosts belonging to different eukaryotic kingdoms, in particular, fungi and plants.
Cristina Rosa - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Ourmiavirus.
Journal of General Virology, 2017Co-Authors: Massimo Turina, Mina Rastgou, Bradley I. Hillman, Keramat Izadpanah, Cristina RosaAbstract:Members of the plant virus genus Ourmiavirus are characterized by having non-enveloped bacilliform virions with a series of discrete lengths from 30 to 62 nm composed of a single coat protein (CP). The genome consists of three positive-sense single-stranded RNAs, each encoding a single protein. The RNA-dependent RNA polymerase (RdRp) has closest similarity to that of viruses from the family Narnaviridae; the movement protein (MP) is similar to the MPs of tombusviruses; the CP shows limited similarity to the CPs of several plant and animal viruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the genus Ourmiavirus, which is available at www.ictv.global/report/Ourmiavirus.
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Identification of Ourmiavirus 30K movement protein amino acid residues involved in symptomatology, viral movement, subcellular localization and tubule formation.
Molecular Plant Pathology, 2016Co-Authors: Paolo Margaria, Charles T Anderson, Massimo Turina, Cristina RosaAbstract:Several plant viruses encode movement proteins (MPs) classified in the 30K superfamily. Despite a great functional diversity, alignment analysis of MP sequences belonging to the 30K superfamily revealed the presence of a central core region, including amino acids potentially critical for MP structure and functionality. We performed alanine-scanning mutagenesis of the Ourmia melon virus (OuMV) MP, and studied the effects of amino acid substitutions on MP properties and virus infection. We identified five OuMV mutants that were impaired in systemic infection in Nicotiana benthamiana and Arabidopsis thaliana, and two mutants showing necrosis and pronounced mosaic symptoms, respectively, in N. benthamiana. Green fluorescent protein fusion constructs (GFP:MP) of movement-defective MP alleles failed to localize in distinct foci at the cell wall, whereas a GFP fusion with wild-type MP (GFP:MPwt) mainly co-localized with plasmodesmata and accumulated at the periphery of epidermal cells. The movement-defective mutants also failed to produce tubular protrusions in protoplasts isolated from infected leaves, suggesting a link between tubule formation and the ability of OuMV to move. In addition to providing data to support the importance of specific amino acids for OuMV MP functionality, we predict that these conserved residues might be critical for the correct folding and/or function of the MP of other viral species in the 30K superfamily.
Michael Arribas Ayllon - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Botourmiaviridae.
The Journal of general virology, 2020Co-Authors: Michael Arribas Ayllon, Shin-yi Lee Marzano, Massimo Turina, Livia Donaire, Jiatao Xie, Luca Nerva, Daohong JiangAbstract:The family Botourmiaviridae includes viruses infecting plants and filamentous fungi containing a positive-sense, ssRNA genome that can be mono- or multi-segmented. Genera in the family include: Ourmiavirus (plant viruses), and Botoulivirus, Magoulivirus and Scleroulivirus (fungal viruses). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the family Botourmiaviridae, which is available at ictv.global/report/botourmiaviridae.
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Molecular characterization of Botrytis ourmia-like virus, a mycovirus close to the plant pathogenic genus Ourmiavirus
Virology, 2016Co-Authors: Livia Donaire, Julio Rozas, Michael Arribas AyllonAbstract:The molecular characterization of a novel single-stranded RNA virus, obtained by next generation sequencing using Illumina platform, in a field grapevine isolate of the plant pathogenic fungus Botrytis, is reported in this work. The sequence comparison of this virus against the NCBI database showed a strong identity with RNA dependent RNA polymerases (RdRps) of plant pathogenic viruses belonging to the genus Ourmiavirus, therefore, this novel virus was named Botrytis ourmia-like virus (BOLV). BOLV has one open reading frame of 2169 nucleotides, which encodes a protein of 722 amino acids showing conserved domains of plant RNA viruses RdRps such as the most conserved GDD active domain. Our analyses showed that BOLV is phylogenetically closer to the fungal Narnavirus and the plant Ourmiavirus than to Mitovirus of the family Narnaviridae. Hence, we proposed that BOLV might represent the link between fungal viruses of the family Narnaviridae and the plant Ourmiaviruses.
