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Buivydaitė Ž, Winding A, Jørgensen LN, Zervas A, Sapkota R. New insights into RNA mycoviruses of fungal pathogens causing Fusarium head blight. Virus Res 2024; 349:199462. [PMID: 39260572 PMCID: PMC11417338 DOI: 10.1016/j.virusres.2024.199462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/13/2024]
Abstract
Fusarium head blight (FHB) continues to be a major problem in wheat production and is considered a disease complex caused by several fungal pathogens including Fusarium culmorum, F. graminearum and F. equiseti. With the objective of investigating diversity of mycoviruses in FHB-associated pathogens, we isolated Fusarium spp. from six wheat (Triticum aestivum) cultivars. In total, 56 Fusarium isolates (29 F. culmorum, 24 F. graminearum, one F. equiseti) were screened for mycoviruses by extracting and sequencing double-stranded RNA. We found that a large proportion of Fusarium isolates (46 %) were infected with mycoviruses. F. culmorum, previously described to harbor only one mycovirus, tended to host more viruses than F. graminearum, with a few isolates harboring seven mycoviruses simultaneously. Based on the RNA-dependent RNA polymerase domain analysis, ten were positive-sense single-stranded RNA viruses (related to viruses from families Mitoviridae, Botourmiaviridae, Narnaviridae, Tymoviridae, Gammaflexiviridae, as well as proposed Ambiguiviridae and ormycovirus viral group), one was double-stranded RNA virus (Partitiviridae), and five were negative-sense single-stranded RNA viruses (related to members in the families of Yueviridae, Phenuiviridae, Mymonaviridae, as well as proposed Mycoaspiviridae). Five mycoviruses were shared between F. graminearum and F. culmorum. These results increase our general understanding of mycovirology. To our knowledge, this is the first in-depth report of the mycovirome in F. culmorum and the first report on the diversity of mycoviruses from Danish isolates of FHB-causing fungi in general.
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Affiliation(s)
- Živilė Buivydaitė
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde 4000, Denmark
| | - Anne Winding
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde 4000, Denmark
| | | | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde 4000, Denmark
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde 4000, Denmark.
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Fan Y, Zhao W, Tang X, Yang M, Yang Y, Zhang Z, Cheng B, Zhou E, He Z. Co-infection of Four Novel Mycoviruses from Three Lineages Confers Hypovirulence on Phytopathogenic Fungus Ustilaginoidea virens. RICE (NEW YORK, N.Y.) 2024; 17:44. [PMID: 39014281 PMCID: PMC11252108 DOI: 10.1186/s12284-024-00721-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/21/2024] [Indexed: 07/18/2024]
Abstract
Rice false smut caused by Ustilaginoidea virens has become one of the most important diseases of rice. Mycoviruses are viruses that can infect fungi with the potential to control fungal diseases. However, little is known about the biocontrol role of hypoviruses in U. virens. In this study, we revealed that the hypovirulence-associated U. virens strain Uv325 was co-infected by four novel mycoviruses from three lineages, designated Ustilaginoidea virens RNA virus 16 (UvRV16), Ustilaginoidea virens botourmiavirus virus 8 (UvBV8), Ustilaginoidea virens botourmiavirus virus 9 (UvBV9), and Ustilaginoidea virens narnavirus virus 13 (UvNV13), respectively. The U. virens strain co-infected by four mycoviruses showed slower growth rates, reduced conidial yield, and attenuated pigmentation. We demonstrated that UvRV16 was not only the major factor responsible for the hypovirulent phenotype in U. vriens, but also able to prevent U. virens to accumulate more mycotoxin, thereby weakening the inhibitory effects on rice seed germination and seedling growth. Additionally, we indicated that UvRV16 can disrupt the antiviral response of U. virens by suppressing the transcriptional expression of multiple genes involved in autophagy and RNA silencing. In conclusion, our study provided new insights into the biological control of rice false smut.
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Affiliation(s)
- Yu Fan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenhua Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaolin Tang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Mei Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yingqing Yang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Zixuan Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Baoping Cheng
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Key Laboratory of Green Prevention and Control On Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong, 510642, China.
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhenrui He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
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He Z, Zhao W, Fan Y, Wang L, Yang M, Yang Y, Zhou E. Genome characterization of a novel narnavirus infecting the plant-pathogenic fungus Ustilaginoidea virens. Arch Virol 2024; 169:78. [PMID: 38517587 DOI: 10.1007/s00705-024-06009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/15/2024] [Indexed: 03/24/2024]
Abstract
Mycoviruses are viruses that infect fungi and oomycetes. They are widespread in all major groups of plant-pathogenic fungi and oomycetes. To date, only the full genome of dsRNA mycoviruses and the contigs of positive-sense single-stranded RNA (+ssRNA) mycoviruses have been reported in Ustilaginoidea virens, which is the notorious causal agent of rice false smut (RFS). Here, we report the molecular characterization of a novel +ssRNA mycovirus, Ustilaginoidea virens narnavirus 4 (UvNV4), isolated from U. virens strain Uv418. UvNV4 has a genome of 3,131 nucleotides (nt) and possesses an open reading frame (ORF) predicted to encode an RNA-dependent RNA polymerase (RdRp) of 1,017 amino acids (aa) sequence with a molecular mass of 116.6 kDa. BLASTp analysis revealed that the RdRp showed 50.34% aa sequence identity to that of the previously described Zhangzhou Narna tick virus 1. Phylogenetic analysis indicated that UvNV4 is closely related to members of the family Narnaviridae. Taken together, these results clearly demonstrate that UvNV4 is a novel +ssRNA virus infecting U. virens.
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Affiliation(s)
- Zhenrui He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenhua Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Fan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Li Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Mei Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yingqing Yang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
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Sahin E, Ozbey Saridogan BG, Keskin E, Akata I. Identification and complete genome sequencing of a novel betapartitivirus naturally infecting the mycorrhizal desert truffle Terfezia claveryi. Virus Genes 2023; 59:254-259. [PMID: 36735175 DOI: 10.1007/s11262-023-01972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Viruses that naturally infect fungal species and capable of establishing mycorrhizae are largely unknown. In this study, we identified and characterized a new partitivirus inhabiting the ascomycete, mycorrhizal desert truffle species Terfezia claveryi, and named it "Terfezia claveryi partitivirus 1" (TcPV1). The entire genome of TcPV1, sequenced by both high throughput sequencing of the total dsRNA extracts and by Sanger sequencing of the RLM-RACE PCR products comprised two dsRNA segments of 2404 bp and 2374 bp, respectively. Both dsRNA genome segments harbored a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. The BLASTp search of the RdRp and CP sequences revealed the highest sequence identities (41.92% and 24.13% identity, respectively) to those of Bipolaris maydis partitivirus 2 and Plasmopara viticola lesion associated partitivirus 5. Molecular phylogenetic analyses of the RdRp sequence showed that TcPV1 fall within a clade composed entirely of members of the genus Betapartitivirus, belonging to the family Partitiviridae. In light of this molecular evidence, TcPV1 is a new member of the genus Betapartitivirus. This is the first report of a new partitivirus hosted by the ascomycete, mycorrhizal fungus T. claveryi.
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Affiliation(s)
- Ergin Sahin
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, 35390, İzmir, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Buca, 35390, İzmir, Turkey.
| | | | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture, Department of Fisheries and Aquaculture, Ankara University, Dışkapı, 06110, Ankara, Turkey
| | - Ilgaz Akata
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey
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Akata I, Edis G, Keskin E, Sahin E. Diverse partitiviruses hosted by the ectomycorrhizal agaric Hebeloma mesophaeum and the natural transmission of a partitivirus between phylogenetically distant, sympatric fungi. Virology 2023; 581:63-70. [PMID: 36913914 DOI: 10.1016/j.virol.2023.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Mycorrhizal fungi host diverse mycoviruses that contribute to our understanding of their diversity and evolution. Here we report on the identification and complete genome characterization of three novel partitiviruses naturally infecting the ectomycorrhizal fungus Hebeloma mesophaeum. During NGS derived viral sequence analyses, we identified a partitivirus that is conspecific with the previously reported partitivirus (LcPV1) described from a saprotrophic fungus Leucocybe candicans. The two distinct fungal specimens inhabited the same vicinity of a campus garden. RdRp sequences encoded by the LcPV1 isolates from both host fungi was found to be identical. Bio-tracking studies revealed that viral loads of LcPV1 drop significantly in L. candicans but not in H. mesophaeum within four years period. The physical proximity of the mycelial networks of both fungal specimens implied the occurrence of a virus transmission event with unknown mechanism. Nature of this virus transmission was discussed in relation to transient interspecific mycelial contact hypothesis.
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Affiliation(s)
- Ilgaz Akata
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey
| | - Gulce Edis
- Ankara University Science Institute, 06110, Dışkapı, Ankara, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, 06110, Dışkapı, Ankara, Turkey
| | - Ergin Sahin
- Dokuz Eylül University Faculty of Science Department of Biology, 35390, Buca, İzmir, Turkey; Dokuz Eylül University Fauna and Flora Research and Application Center, 35390, Buca, İzmir, Turkey.
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Shamsi W, Kondo H, Ulrich S, Rigling D, Prospero S. Novel RNA viruses from the native range of Hymenoscyphus fraxineus, the causal fungal agent of ash dieback. Virus Res 2022; 320:198901. [PMID: 36058013 DOI: 10.1016/j.virusres.2022.198901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022]
Abstract
The native Japanese population of the fungus Hymenoscyphus fraxineus, the causal agent of ash dieback in Europe, was screened for viruses using a high-throughput sequencing method. Five RNA viruses were detected in 116 fungal isolates sequenced via Illumina RNA-seq platform, with an overall virus prevalence of 11.2%. The viruses were completely sequenced by RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) followed by Sanger sequencing. The sequences appear to represent new species from three established families (Mito-, Endorna- and Partitiviridae), one recognized genus (Botybirnavirus) and a negative-sense single-stranded RNA virus in the order Bunyavirales from the proposed family "Mybuviridae". The highest prevalence was found for the mitovirus (7.8%), that had two genomic forms (linear and circular), while the other viruses were detected each in one isolate. Co-infection of a mitovirus and an endornavirus was also observed in one of the infected isolates. Here we describe the molecular characterization of the identified viruses. This study expands the diversity of viruses in H. fraxineus and provides the basis for investigating the virus-mediated control of ash dieback in Europe.
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Affiliation(s)
- Wajeeha Shamsi
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Sven Ulrich
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Daniel Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
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Full genome sequence of a new three-segment gammapartitivirus from the phytopathogenic fungus Alternaria tenuissima on cotton in China. Arch Virol 2021; 166:973-976. [PMID: 33427965 DOI: 10.1007/s00705-020-04937-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/10/2020] [Indexed: 10/22/2022]
Abstract
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.
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Filippou C, Coutts RHA, Stevens DA, Sabino R, Kotta-Loizou I. Completion of the sequence of the Aspergillus fumigatus partitivirus 1 genome. Arch Virol 2020; 165:1891-1894. [PMID: 32458177 PMCID: PMC7351820 DOI: 10.1007/s00705-020-04660-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 04/12/2020] [Indexed: 11/26/2022]
Abstract
A Portuguese isolate of Aspergillus fumigatus was found to contain three double-stranded (ds) RNA elements ranging in size from 1.1 to 1.8 kbp and comprising the genome of a strain of Aspergillus fumigatus partitivirus 1 (AfuPV-1) previously thought to contain only the two largest dsRNA elements. The sequence of the smallest dsRNA element is described here, completing the sequence of the AfuPV-1 genome. Sequence analysis of the element revealed an open reading frame encoding a protein of unknown function similar in size and distantly related to elements previously identified in other members of the family Partitiviridae.
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Affiliation(s)
- Charalampos Filippou
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK
| | - Robert H A Coutts
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK
| | - David A Stevens
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
- California Institute for Medical Research, San Jose, California, USA
| | - Raquel Sabino
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.
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A novel monopartite dsRNA virus isolated from the phytopathogenic fungus Ustilaginoidea virens strain GZ-2. Arch Virol 2018; 163:3427-3431. [DOI: 10.1007/s00705-018-3976-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
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Kotta-Loizou I, Coutts RHA. Mycoviruses in Aspergilli: A Comprehensive Review. Front Microbiol 2017; 8:1699. [PMID: 28932216 PMCID: PMC5592211 DOI: 10.3389/fmicb.2017.01699] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/23/2017] [Indexed: 12/31/2022] Open
Abstract
Fungi, similar to all species, are susceptible to viral infection. Aspergillus is arguably the most well studied fungal genus because of its medical, ecological and economical significance. Mycoviruses were initially detected in Aspergillus species almost 50 years ago and the field continues to be active today with ground-breaking discoveries. The aim of the present review is to cover the scientific progress in all aspects of mycovirology as exemplified by Aspergillus-focused research. Initially an overview of the population studies illustrating the presence of mycoviruses in numerous important Aspergillus species, such as A. niger, A. flavus, and A. fumigatus with be presented. Moreover the intricacies of mycovirus transmission, both inter- and intra-species, will be discussed together with the methodologies used to investigate viral dispersion in a laboratory setting. Subsequently, the genomic features of all molecularly characterized mycoviruses to date will be analyzed in depth. These include members of established viral families, such as Partitiviridae, Chrysoviridae and Totiviridae, but also more recent, novel discoveries that led to the proposal of new viral families, such as Polymycoviridae, Alternaviridae and, in the context of the present review, Exartaviridae. Finally, the major issue of phenotypic effects of mycoviral infection on the host is addressed, including aflatoxin production in A. flavus, together with growth and virulence in A. fumigatus. Although the molecular mechanisms behind these phenomena are yet to be elucidated, recent studies suggest that by implication, RNA silencing may be involved.
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Affiliation(s)
- Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College LondonLondon, United Kingdom
| | - Robert H A Coutts
- Department of Biological and Environmental Sciences, University of HertfordshireHatfield, United Kingdom
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Mycoviruses in the Plant Pathogen Ustilaginoidea virens Are Not Correlated with the Genetic Backgrounds of Its Hosts. Int J Mol Sci 2017; 18:ijms18050963. [PMID: 28467379 PMCID: PMC5454876 DOI: 10.3390/ijms18050963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/21/2017] [Accepted: 04/26/2017] [Indexed: 11/27/2022] Open
Abstract
Ustilaginoidea virens, the causal agent of rice false smut, is one of the most devastating grain diseases that causes loss of yield in most rice-growing areas worldwide. In this study, we performed a dsRNA screen to isolate mycoviruses from 35 U. virens strains. The results revealed that 34 of the tested isolates were infected by various dsRNA elements, displaying highly viral diversity and mixed infections. We characterized a 5.3 kbp dsRNA from a typical isolate containing dsRNA segments with sizes ranging from 0.5 to 5.3 kbp. Sequence analysis of its genomic properties indicated that it is a novel victorivirus, named Ustilaginoidea virens RNA virus 5 (UvRV5), that belongs to the family Totiviridae. RT-PCR detection was performed and indicated that not all the dsRNA bands that were 5.3 kbp in size contained UvRV5. Moreover, the genetic relatedness of all the U. virens strains was estimated according to phylogenetic analysis of the partial intergenic spacer region (IGS) sequences. However, concordance was not found between the dsRNA profiles and the IGS-based genetic relatedness of their host fungi.
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Fan J, Yang J, Wang Y, Li G, Li Y, Huang F, Wang W. Current understanding on Villosiclava virens, a unique flower-infecting fungus causing rice false smut disease. MOLECULAR PLANT PATHOLOGY 2016; 17:1321-1330. [PMID: 26720072 PMCID: PMC6638446 DOI: 10.1111/mpp.12362] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 12/25/2015] [Accepted: 12/27/2015] [Indexed: 05/13/2023]
Abstract
Villosiclava virens (Vv) is an ascomycete fungal pathogen that causes false smut disease in rice. Recent reports have revealed some interesting aspects of the enigmatic pathogen to address the question of why it specifically infects rice flowers and converts a grain into a false smut ball. Comparative and functional genomics have suggested specific adaptation of Vv in the colonization of rice flowers. Anatomical studies have disclosed that Vv specifically infects rice stamen filaments before heading and intercepts seed formation. In addition, Vv can occupy the whole inner space of a spikelet embracing all floral organs and activate the rice grain-filling network, presumably for nutrient acquisition to support the development of the false smut ball. This profile provides a general overview of the rice false smut pathogen, and summarizes advances in the Vv life cycle, genomics and genetics, and the molecular Vv-rice interaction. Current understandings of the Vv-rice pathosystem indicate that it is a unique and interesting system which can enrich the study of plant-pathogen interactions. Taxonomy: Ustilaginoidea virens is the anamorph form of the pathogen (Kingdom Fungi; Phylum Ascomycota; Class Ascomycetes; Subclass Incertae sedis; Order Incertae sedis; Family Incertae sedis; Genus Ustilaginoidea). The teleomorph form is Villosiclava virens (Kingdom Fungi; Phylum Ascomycota; Class Ascomycetes; Subclass Sordariomycetes; Order Hypocreales; Family Clavicipitaceae; Genus Villosiclava). Disease symptoms: The only visible symptom is the replacement of rice grains by ball-shaped fungal mycelia, namely false smut balls. When maturing, the false smut ball is covered with powdery chlamydospores, and the colour changes to yellowish, yellowish orange, green, olive green and, finally, to greenish black. Sclerotia are often formed on the false smut balls in autumn. Identification and detection: Vv conidia are round to elliptical, measuring 3-5 μm in diameter. Chlamydospores are ornamented with prominent irregularly curved spines, which are 200-500 nm in length. The sclerotia are black, horseshoe-shaped and irregular oblong or flat, ranging from 2 to 20 mm. Nested polymerase chain reaction (PCR) and quantitative PCR have been developed to specifically detect Vv presence in rice tissues and other biotic and abiotic samples in fields. Host range: Rice is the primary host for Vv. Natural infection by Vv has been found on several paddy field weeds, including Digitaria marginata, Panicum trypheron, Echinochloa crusgalli and Imperata cylindrica. However, the occurrence of infection in these potential alternative hosts is very rare. Life cycle: Vv infects rice spikelets at the late rice booting stage, and produces false smut balls covered with dark-green chlamydospores. Occasionally, sclerotia form on the surface of false smut balls in late autumn when the temperature fluctuates greatly between day and night. Both chlamydospores and sclerotia may serve as primary infection sources. Rainfall at the rice booting stage is a major environmental factor resulting in epidemics of rice false smut disease. Disease control: The use of fungicides is the major approach for the control of Vv. Several fungicides, such as cuproxat SC, copper oxychloride, tebuconazole, propiconazole, difenoconazole and validamycin, are often applied. However, the employment of resistant rice cultivars and genes has been limited, because of the poor understanding of rice resistance to Vv. Useful websites: Villosiclava virens genome sequence: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JHTR01#contigs.
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Affiliation(s)
- Jing Fan
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Juan Yang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Yu‐Qiu Wang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Guo‐Bang Li
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Yan Li
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Fu Huang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
- College of Agronomy & Institute of Agricultural EcologySichuan Agricultural UniversityChengdu611130China
| | - Wen‐Ming Wang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
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A novel mycovirus identified from the rice false smut fungus Ustilaginoidea virens. Virus Genes 2015; 51:159-62. [PMID: 26041139 DOI: 10.1007/s11262-015-1212-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
Abstract
The complete sequence of a novel mycovirus infecting Ustilaginoidea virens, the causal agent of false smut of rice, is reported here and designated as Ustilaginoidea virens unassigned RNA virus HNND-1 (UvURV-HNND-1). This virus has an undivided dsRNA genome of 2903 nt in length and contains two non-overlapping open reading frames (ORF1 and 2), with the small ORF1 encoding a protein of unknown function that showed sequence similarity to the comparable protein in virus Alternaria longipes dsRNA virus 1(AlRV1) and a larger ORF2 encoded the protein showing identities to the RNA-dependent RNA polymerases of AlRV1 and some other unassigned dsRNA viruses. Phylogenetic analysis showed that UvURV-HNND-1 is more closely related to unclassified viruses such as AlRV1 and distinct from distantly related members of the family Partitiviridae. Here, we propose in accordance with previous reports that UvURV-HNND-1 might belong to a new mycovirus genus together with AlRV1 and other similar viruses.
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Liu L, Wang Q, Cheng J, Fu Y, Jiang D, Xie J. Molecular characterization of a bipartite double-stranded RNA virus and its satellite-like RNA co-infecting the phytopathogenic fungus Sclerotinia sclerotiorum. Front Microbiol 2015; 6:406. [PMID: 25999933 PMCID: PMC4422086 DOI: 10.3389/fmicb.2015.00406] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022] Open
Abstract
A variety of mycoviruses have been found in Sclerotinia sclerotiorum. In this study, we report a novel mycovirus S. sclerotiorum botybirnavirus 1 (SsBRV1) that was originally isolated from the hypovirulent strain SCH941 of S. sclerotiorum. SsBRV1 has rigid spherical virions that are ∼38 nm in diameter, and three double-stranded RNA (dsRNA) segments (dsRNA1, 2, and 3 with lengths of 6.4, 6.0, and 1.7 kbp, respectively) were packaged in the virions. dsRNA1 encodes a cap-pol fusion protein, and dsRNA2 encodes a polyprotein with unknown functions but contributes to the formation of virus particles. The dsRNA3 is dispensable and may be a satellite-like RNA of SsBRV1. Although phylogenetic analysis of the RdRp domain demonstrated that SsBRV1 is related to Botrytis porri RNA virus 1 (BpRV1) and Ustilago maydis dsRNA virus-H1, the structure proteins of SsBRV1 do not have any significant sequence similarities with other known viral proteins with the exception of those of BpRV1. SsBRV1 carrying dsRNA3 seems to have no obvious effects on the colony morphology, but can significantly reduce the growth rate and virulence of S. sclerotiorum. These findings provide new insights into the virus taxonomy, virus evolution and the interactions between SsBRV1 and the fungal hosts.
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Affiliation(s)
- Lijiang Liu
- State Key Laboratory of Agricultural Microbiology and The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Qihua Wang
- State Key Laboratory of Agricultural Microbiology and The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology and The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Yanping Fu
- State Key Laboratory of Agricultural Microbiology and The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology and The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology and The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
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Prevalence and diversity of mycoviruses infecting the plant pathogen Ustilaginoidea virens. Virus Res 2015; 195:47-56. [DOI: 10.1016/j.virusres.2014.08.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 12/15/2022]
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Nibert ML, Ghabrial SA, Maiss E, Lesker T, Vainio EJ, Jiang D, Suzuki N. Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research. Virus Res 2014; 188:128-41. [DOI: 10.1016/j.virusres.2014.04.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
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Zhong J, Lei XH, Zhu JZ, Song G, Zhang YD, Chen Y, Gao BD. Detection and sequence analysis of two novel co-infecting double-strand RNA mycoviruses in Ustilaginoidea virens. Arch Virol 2014; 159:3063-70. [DOI: 10.1007/s00705-014-2144-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/31/2014] [Indexed: 11/28/2022]
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Zhong J, Zhou Q, Lei XH, Chen D, Shang HH, Zhu HJ. The nucleotide sequence and genome organization of two victoriviruses from the rice false smut fungus Ustilaginoidea virens. Virus Genes 2014; 48:570-3. [DOI: 10.1007/s11262-014-1050-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/08/2014] [Indexed: 01/11/2023]
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Complete genome sequence and organization of a novel virus from the rice false smut fungus Ustilaginoidea virens. Virus Genes 2014; 48:329-33. [PMID: 24510355 DOI: 10.1007/s11262-013-1022-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 11/29/2013] [Indexed: 10/25/2022]
Abstract
In this study, three dsRNA segments from the rice false smut fungus Ustilaginoidea virens, the causal agent of a serious disease in rice, with molecular size ranging from 1.3 to 5 Kb, were isolated and named as dsRNA-L, dsRNA-M, and dsRNA-S. The complete nucleotide sequences of dsRNA-M and dsRNA-S were determined and analyzed. The dsRNA-M putatively encodes an RNA-dependent RNA polymerase, which is similar to that of the partitiviruses in the family Partitiviridae. Although the protein encoded by dsRNA-S showed less similarity to the typical coat protein of the virus in the family Partitiviridae, the structural analysis results indicated that the dsRNA-S might function as the capsid protein. We propose that the virus is Ustilaginoidea virens partitivirus 2-Uv0901, a new member, but distantly related to the newly proposed genus Gammapartitivirus with a distinct sequence pattern of capsid protein.
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Jiang Y, Luo C, Jiang D, Li G, Huang J. The complete genomic sequence of a second novel partitivirus infecting Ustilaginoidea virens. Arch Virol 2014; 159:1865-8. [PMID: 24473710 DOI: 10.1007/s00705-014-1991-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/14/2014] [Indexed: 11/28/2022]
Abstract
The bisegmented genome of a putative double-stranded (ds) RNA virus from Ustilaginoidea virens was sequenced and analyzed. The larger genomic segment of 2112 bp encodes a putative RNA-dependent RNA polymerase (RdRp, 628 aa), and the smaller one of 2082 bp encodes a putative coat protein (CP) of 539 aa. The 5' untranslated regions (UTR) of the two segments share regions of high sequence homology. Phylogenetic analysis indicates that this novel partitivirus, named Ustilaginoidea virens partitivirus 2 (UvPV2), can be assigned to the family Partitiviridae.
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Affiliation(s)
- Yinhui Jiang
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Xie J, Jiang D. New insights into mycoviruses and exploration for the biological control of crop fungal diseases. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:45-68. [PMID: 25001452 DOI: 10.1146/annurev-phyto-102313-050222] [Citation(s) in RCA: 288] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
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.
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Affiliation(s)
- Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China;
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