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Yang Z, Zhang B, Hu Y, Zhao L, Chen Z, Zhong J, Su J, Chen Y. Molecular characterization of a novel gammapartitivirus infecting the fungus Nigrospora oryzae. Arch Virol 2024; 169:188. [PMID: 39187668 DOI: 10.1007/s00705-024-06111-6] [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: 07/03/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024]
Abstract
Here, we identified a new mycovirus infecting the phytopathogenic fungus Nigrospora oryzae, which we have designated "Nigrospora oryzae partitivirus 2" (NoPV2). The genome of NoPV2 consists of two dsRNA segments (dsRNA 1 and dsRNA 2), measuring 1771 and 1440 bp in length, respectively. dsRNA 1 and dsRNA 2 each contain a single open reading frame (ORF) that encodes the RNA-dependent RNA polymerase (RdRp) and capsid protein (CP), respectively. A BLASTp search showed that the RdRp of NoPV2 had significant sequence similarity to the RdRps of other partitiviruses, including Nigrospora sphaerica partitivirus 1 (75.61% identity) and Magnaporthe oryzae partitivirus 1 (67.53% identity). Phylogenetic analysis revealed that NoPV2 is a new member of the genus Gammapartitivirus in the family Partitiviridae. This study provides important information for understanding the diversity of mycoviruses in N. oryzae.
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Affiliation(s)
- Zhijuan Yang
- Dali Tobacco Company of Yunnan Province, Dali City, Yunnan Province, 671000, P.R. China
| | - Baolin Zhang
- Qujing Tobacco Company of Yunnan Province, Qujing Yunnan Province, 655000, P.R. China
| | - Yang Hu
- Chuxiong Company of Yunnan Provincial Tobacco Corporation, Chuxiong, 675000, P.R. China
| | - Lianjing Zhao
- Chuxiong Company of Yunnan Provincial Tobacco Corporation, Chuxiong, 675000, P.R. China
| | - Zengmin Chen
- Chuxiong Company of Yunnan Provincial Tobacco Corporation, Chuxiong, 675000, P.R. China
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha City, Hunan Province, 410128, P.R. China
| | - Jiaen Su
- Dali Tobacco Company of Yunnan Province, Dali City, Yunnan Province, 671000, P.R. China.
| | - Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan Province, 650021, P.R. China.
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Urzo MLR, Guinto TD, Eusebio-Cope A, Budot BO, Yanoria MJT, Jonson GB, Arakawa M, Kondo H, Suzuki N. Metatranscriptomic Sequencing of Sheath Blight-Associated Isolates of Rhizoctonia solani Revealed Multi-Infection by Diverse Groups of RNA Viruses. Viruses 2024; 16:1152. [PMID: 39066314 PMCID: PMC11281561 DOI: 10.3390/v16071152] [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: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Rice sheath blight, caused by the soil-borne fungus Rhizoctonia solani (teleomorph: Thanatephorus cucumeris, Basidiomycota), is one of the most devastating phytopathogenic fungal diseases and causes yield loss. Here, we report on a very high prevalence (100%) of potential virus-associated double-stranded RNA (dsRNA) elements for a collection of 39 fungal strains of R. solani from the rice sheath blight samples from at least four major rice-growing areas in the Philippines and a reference isolate from the International Rice Research Institute, showing different colony phenotypes. Their dsRNA profiles suggested the presence of multiple viral infections among these Philippine R. solani populations. Using next-generation sequencing, the viral sequences of the three representative R. solani strains (Ilo-Rs-6, Tar-Rs-3, and Tar-Rs-5) from different rice-growing areas revealed the presence of at least 36 viruses or virus-like agents, with the Tar-Rs-3 strain harboring the largest number of viruses (at least 20 in total). These mycoviruses or their candidates are believed to have single-stranded RNA or dsRNA genomes and they belong to or are associated with the orders Martellivirales, Hepelivirales, Durnavirales, Cryppavirales, Ourlivirales, and Ghabrivirales based on their coding-complete RNA-dependent RNA polymerase sequences. The complete genome sequences of two novel RNA viruses belonging to the proposed family Phlegiviridae and family Mitoviridae were determined.
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Affiliation(s)
- Michael Louie R. Urzo
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.L.R.U.); (T.D.G.)
| | - Timothy D. Guinto
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.L.R.U.); (T.D.G.)
| | - Ana Eusebio-Cope
- Fit-for-Future Genetic Resources Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Bernard O. Budot
- Institute of Weed Science, Entomology, and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines;
| | - Mary Jeanie T. Yanoria
- Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.J.T.Y.); (G.B.J.)
| | - Gilda B. Jonson
- Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines; (M.J.T.Y.); (G.B.J.)
| | - Masao Arakawa
- Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan;
| | - Hideki Kondo
- Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
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Zhao Y, Zhang X, Mu T, Wu X. Complete genome sequence of a novel partitivirus with a dsRNA3 segment, isolated from Fusarium commune strain CP-SX-3 causing strawberry root rot. Arch Virol 2024; 169:60. [PMID: 38430446 DOI: 10.1007/s00705-024-06004-8] [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: 11/12/2023] [Accepted: 01/24/2024] [Indexed: 03/03/2024]
Abstract
A novel partitivirus, Fusarium commune partitivirus 1 (FcoPV1), was identified in Fusarium commune strain CP-SX-3 isolated from diseased roots of strawberry with symptoms of root rot. The complete genome of FcoPV1 comprises three double-stranded RNAs (dsRNAs): dsRNA1 (1,825 nt), dsRNA2 (1,592 nt), and dsRNA3 (1,421 nt). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), and dsRNA2 contains a single ORF (ORF2) encoding a coat protein (CP). dsRNA3 is a possible satellite RNA that does not appear to encode a known protein. BLASTp analysis revealed that RdRp (86.59%) and CP (74.13%) encoded by the two ORFs (ORF1 and ORF2) had the highest sequence similarity to their counterparts in Fusarium equiseti partitivirus 1 (FePV1). Phylogenetic analysis based on the complete amino acid sequence of RdRp suggested that FcoPV1 should be considered a member of a new species in the proposed genus "Zetapartitivirus" within the family Partitiviridae. To the best of our knowledge, this is the first report of a zetapartitivirus infecting phytopathogenic F. commune.
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Affiliation(s)
- Yumeng Zhao
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
- Liaoning Institute of Pomology, Yingkou City, Liaoning, 115009, People's Republic of China
| | - Xinyi Zhang
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Tongyu Mu
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
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Zhu JZ, Qiu ZL, Gao BD, Li XG, Zhong J. A novel partitivirus conferring hypovirulence by affecting vesicle transport in the fungus Colletotrichum. mBio 2024; 15:e0253023. [PMID: 38193704 PMCID: PMC10865989 DOI: 10.1128/mbio.02530-23] [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: 09/17/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024] Open
Abstract
Colletotrichum spp. are economically important phytopathogenic fungi that cause anthracnose in a variety of plant species worldwide. Hypovirulence-associated mycoviruses provide new options for the biological control of plant fungal diseases. Here, we found a novel partitivirus from Colletotrichum alienum and named it Colletotrichum alienum partitivirus 1 (CaPV1). CaPV1 contained two dsRNA segments encoding an RNA-dependent RNA polymerase and a capsid protein and was classified under the genus Gammapartitivirus of the family Partitiviridae. CaPV1 significantly decreased host virulence, mycelial growth, appressorial development, and appressorium turgor but increased conidial production with abnormal morphology. In addition, CaPV1 could be successfully transfected into other Colletotrichum species, including C. fructicola, C. spaethianum, and C. gloeosporioides, and caused hypovirulence, indicating the broad application potential of this virus. CaPV1 caused significant transcriptional rewiring of the host fungus C. alienum. Notably, some genes related to vesicle transport in the CaPV1-infected strain were downregulated, consistent with the impaired endocytosis pathway in this fungus. When the Rab gene CaRab7, which is associated with endocytosis in vesicle transport, was knocked out, the virulence of the mutants was reduced. Overall, our findings demonstrated that CaPV1 has the potential to control anthracnose caused by Colletotrichum, and the mechanism by which Colletotrichum induces hypovirulence is caused by affecting vesicle transport.IMPORTANCEColletotrichum is a kind of economically important phytopathogenic fungi that cause anthracnose disease in a variety of plant species worldwide. We found a novel mycovirus of the Gammapartitivirus genus and Partitiviridae family from the phytopathogenic fungus Colletotrichum alienum and named it CaPV1. This study revealed that CaPV1 infection significantly decreased host virulence and fitness by affecting mycelial growth, appressorial development, and appressorium turgor. In addition, CaPV1 could also infect other Colletotrichum species, including C. fructicola, C. spaethianum, and C. gloeosporioides, by viral particle transfection and resulting in hypovirulence of these Colletotrichum species. Transcriptomic analysis showed that CaPV1 caused significant transcriptional rewiring of the host fungus C. alienum, especially the genes involved in vesicle transport. Moreover, endocytosis and gene knockout assays demonstrated that the mechanism underlying CaPV1-induced hypovirulence is, at least in part, caused by affecting the vesicle transport of the host fungus. This study provided insights into the mechanisms underlying the pathogenesis of Colletotrichum species and mycovirus-fungus interactions, linking the role of mycovirus and fungus vesicle transport systems in shaping fungal pathogenicity.
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Affiliation(s)
- Jun Zi Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Ze Lan Qiu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Bi Da Gao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiao Gang Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
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Forgia M, Daghino S, Chiapello M, Ciuffo M, Turina M. New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes. Virus Evol 2024; 10:veae003. [PMID: 38361818 PMCID: PMC10868552 DOI: 10.1093/ve/veae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Recent advances in high throughput sequencing (HTS) approaches allowed a broad exploration of viromes from different fungal hosts, unveiling a great diversity of mycoviruses with interesting evolutionary features. The word mycovirus historically applies also to viruses infecting oomycetes but most studies are on viruses infecting fungi, with less mycoviruses found and characterized in oomycetes, particularly in the obligatory biotrophs. We, here, describe the first virome associated to Bremia lactucae, the causal agent of lettuce downy mildew, which is an important biotrophic pathogen for lettuce production and a model system for the molecular aspects of the plant-oomycetes interactions. Among the identified viruses, we could detect (1) two new negative sense ssRNA viruses related to the yueviruses, (2) the first example of permuted RdRp in a virus infecting fungi/oomycetes, (3) a new group of bipartite dsRNA viruses showing evidence of recent bi-segmentation and concomitantly, a possible duplication event bringing a bipartite genome to tripartite, (4) a first representative of a clade of viruses with evidence of recombination between distantly related viruses, (5) a new open reading frame (ORF)an virus encoding for an RdRp with low homology to known RNA viruses, and (6) a new virus, belonging to riboviria but not conserved enough to provide a conclusive phylogenetic placement that shows evidence of a recombination event between a kitrinoviricota-like and a pisuviricota-like sequence. The results obtained show a great diversity of viruses and evolutionary mechanisms previously unreported for oomycetes-infecting viruses, supporting the existence of a large diversity of oomycetes-specific viral clades ancestral of many fungal and insect virus clades.
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Affiliation(s)
| | - Stefania Daghino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada Delle Cacce 73, Torino 10135, Italy
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada Delle Cacce 73, Torino 10135, Italy
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada Delle Cacce 73, Torino 10135, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada Delle Cacce 73, Torino 10135, Italy
- Institute for Sustainable Plant Protection, National Research Council of Italy, Via Branze 39, Brescia 25123, Italy
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Hassan S, Syun-ichi U, Shabeer S, Wu CF, Moriyama H, Coutts RHA, Kotta-Loizou I, Jamal A. Molecular and biological characterization of a partitivirus from Paecilomyces variotii. J Gen Virol 2023; 104:001925. [PMID: 38015047 PMCID: PMC10768695 DOI: 10.1099/jgv.0.001925] [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: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
Paeciliomyces variotii is a thermo-tolerant, ubiquitous fungus commonly found in food products, indoor environments, soil and clinical samples. It is a well-known biocontrol agent used against phytopathogenic fungi and its metabolites have many industrial applications. Rare reports of P. variotii-related human infections have been found in the medical literature. In this study, we report for the first time the infection of P. variotii isolated from a soil sample collected in a rice field with a double-stranded RNA virus, Paeciliomyces variotii partitivirus 1 (PvPV-1) in the family Partitiviridae. P. variotii harboured icosahedral virus particles 30 nm in diameter with two dsRNA segments 1758 and 1356 bp long. Both dsRNA1 and dsRNA2 have a single open reading frame encoding proteins of 63 and 40 kDa, respectively. These proteins have significant similarity to the RNA-dependent RNA polymerase and capsid protein encoded by the genomic segments of several viruses from the family Partitiviridae. Phylogenetic analysis revealed that PvPV-1 belongs to the family Partitiviridae but in an unclassified group/genus, tentatively nominated Zetapartitivirus. PvPV-1 was found to increase the growth rate of the host fungus, as indicated by time course experiments performed on a range of different media for virus-infected and virus-free isogenic lines. Further, dual-culture assays performed for both isogenic lines confirmed the antagonistic potential of P. variotii against other phytopathogenic fungi. The findings of this study assist us in understanding P. variotii as a potential biocontrol agent, together with plant-fungus-virus interactions.
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Affiliation(s)
- Sidra Hassan
- Department of Plant and Environmental Protection, PARC Institute of Advanced Studies in Agriculture (Affiliated with Quaid-i-Azam University), National Agricultural Research Centre, Islamabad, 45500, Pakistan
| | - Urayama Syun-ichi
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Saba Shabeer
- Department of Bioscience, COMSATS University, Islamabad, 44000, Pakistan
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Chien-Fu Wu
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8, Saiwaicho, Fuchu, Tokyo 184-8509, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8, Saiwaicho, Fuchu, Tokyo 184-8509, Japan
| | - Robert H. A. Coutts
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Ioly Kotta-Loizou
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Atif Jamal
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
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Khan HA, Nerva L, Bhatti MF. The good, the bad and the cryptic: The multifaceted roles of mycoviruses and their potential applications for a sustainable agriculture. Virology 2023; 585:259-269. [PMID: 37453341 DOI: 10.1016/j.virol.2023.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Mycoviruses are natural inhabitants of fungi and have been identified in almost all fungal taxonomic groups. Mycoviruses that infect phytopathogenic fungi are now becoming a hot research area due to their potential for the biocontrol of important plant pathogens. But, before considering a mycovirus for biocontrol, we should be fully aware of the effects it induces in a fungal host and its interactions with other viruses, fungal strains and even the host plants. Mycoviral infections are generally associated with different effects, ranging from hypovirulence to hypervirulence, but they can often be cryptic (latent infections). The cryptic lifestyle has been associated to many mycoviruses, but thanks to growing knowledge we are now aware that it is often associated to axenic conditions while the real effects can be observed only in nature. Other mycoviruses either promote (hypervirulence) or (hypovirulence) fungal pathogenicity by a strong impact on the fungal physiology or by blocking the production of toxins or effectors. Finally, indirect effects of mycoviral infections can also be provided to the plant that hosts the fungal isolate, highlighting not only their potential as direct biocontrol agents but also as priming agents for plant resilience to biotic and abiotic stresses. This review provides a broad overview of mycoviral interactions both with their hosts and with other mycoviruses, highlighting the most interesting examples. In contrast to what has been observed to date, we believe that the collective availability of these data will not only improve our understanding of mycoviruses, but also increase our confidence in considering them as alternative measures against fungal diseases to improve the sustainable production of food and feed commodities.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan; Department of Biotechnology, University of Mianwali, Punjab, 42200, Pakistan
| | - Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile, 31015, Conegliano, (TV), Italy.
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
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Jaccard A, Dubuis N, Kellenberger I, Brodard J, Schnee S, Gindro K, Schumpp O. New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus. J Gen Virol 2023; 104:001879. [PMID: 37549001 PMCID: PMC10539651 DOI: 10.1099/jgv.0.001879] [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: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5' and 3' end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of Gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.
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Affiliation(s)
| | - Nathalie Dubuis
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | | | - Justine Brodard
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Sylvain Schnee
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Katia Gindro
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Department of Plant Protection, Agroscope, Nyon, Switzerland
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Taggart NT, Crabtree AM, Creagh JW, Bizarria R, Li S, de la Higuera I, Barnes JE, Shipley MA, Boyer JM, Stedman KM, Ytreberg FM, Rowley PA. Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae. PLoS Pathog 2023; 19:e1011418. [PMID: 37285383 PMCID: PMC10281585 DOI: 10.1371/journal.ppat.1011418] [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: 10/26/2022] [Revised: 06/20/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.
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Affiliation(s)
- Nathan T Taggart
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Angela M Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jack W Creagh
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Rodolfo Bizarria
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Shunji Li
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Ignacio de la Higuera
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - Jonathan E Barnes
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
| | - Mason A Shipley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Josephine M Boyer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Kenneth M Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - F Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Department of Physics, University of Idaho, Moscow, Idaho, United States of America
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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Wang P, Yang G, Shi N, Zhao C, Hu F, Coutts RHA, Kotta-Loizou I, Huang B. A novel partitivirus orchestrates conidiation, stress response, pathogenicity, and secondary metabolism of the entomopathogenic fungus Metarhizium majus. PLoS Pathog 2023; 19:e1011397. [PMID: 37216409 DOI: 10.1371/journal.ppat.1011397] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/01/2023] [Indexed: 05/24/2023] Open
Abstract
Mycoviruses are widely present in all major groups of fungi but those in entomopathogenic Metarhizium spp. remain understudied. In this investigation, a novel double-stranded (ds) RNA virus is isolated from Metarhizium majus and named Metarhizium majus partitivirus 1 (MmPV1). The complete genome sequence of MmPV1 comprises two monocistronic dsRNA segments (dsRNA 1 and dsRNA 2), which encode an RNA-dependent RNA polymerase (RdRp) and a capsid protein (CP), respectively. MmPV1 is classified as a new member of the genus Gammapartitivirus in the family Partitiviridae based on phylogenetic analysis. As compared to an MmPV1-free strain, two isogenic MmPV1-infected single-spore isolates were compromised in terms of conidiation, and tolerance to heat shock and UV-B irradiation, while these phenotypes were accompanied by transcriptional suppression of multiple genes involved in conidiation, heat shock response and DNA damage repair. MmPV1 attenuated fungal virulence since infection resulted in reduced conidiation, hydrophobicity, adhesion, and cuticular penetration. Additionally, secondary metabolites were significantly altered by MmPV1 infection, including reduced production of triterpenoids, and metarhizins A and B, and increased production of nitrogen and phosphorus compounds. However, expression of individual MmPV1 proteins in M. majus had no impact on the host phenotype, suggesting insubstantive links between defective phenotypes and a single viral protein. These findings indicate that MmPV1 infection decreases M. majus fitness to its environment and its insect-pathogenic lifestyle and environment through the orchestration of the host conidiation, stress tolerance, pathogenicity, and secondary metabolism.
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Affiliation(s)
- Ping Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Guogen Yang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Najie Shi
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Cheng Zhao
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Fenglin Hu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Robert H A Coutts
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
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11
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Zhao C, Li S, Ma Z, Wang W, Gao L, Han C, Yang A, Wu X. Anastomosis Groups and Mycovirome of Rhizoctonia Isolates Causing Sugar Beet Root and Crown Rot and Their Sensitivity to Flutolanil, Thifluzamide, and Pencycuron. J Fungi (Basel) 2023; 9:jof9050545. [PMID: 37233256 DOI: 10.3390/jof9050545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Anastomosis groups (AGs) or subgroups of 244 Rhizoctonia isolates recovered from sugar beet roots with symptoms of root and crown rot were characterized to be AG-A, AG-K, AG-2-2IIIB, AG-2-2IV, AG-3 PT, AG-4HGI, AG-4HGII, and AG-4HGIII, with AG-4HGI (108 isolates, 44.26%) and AG-2-2IIIB (107 isolates, 43.85%) being predominate. Four unclassified mycoviruses and one hundred and one putative mycoviruses belonging to six families, namely Mitoviridae (60.00%), Narnaviridae (18.10%), Partitiviridae (7.62%), Benyviridae (4.76%), Hypoviridae (3.81%), and Botourmiaviridae (1.90%), were found to be present in these 244 Rhizoctonia isolates, most of which (88.57%) contained positive single-stranded RNA genome. The 244 Rhizoctonia isolates were all sensitive to flutolanil and thifluzamide, with average median effective concentration (EC50) value of 0.3199 ± 0.0149 μg·mL-1 and 0.1081 ± 0.0044 μg·mL-1, respectively. Among the 244 isolates, except for 20 Rhizoctonia isolates (seven isolates of AG-A and AG-K, one isolate of AG-4HGI, and 12 isolates of AG-4HGII), 117 isolates of AG-2-2IIIB, AG-2-2IV, AG-3 PT, and AG-4HGIII, 107 isolates of AG-4HGI, and six isolates of AG-4HGII were sensitive to pencycuron, with average EC50 value of 0.0339 ± 0.0012 μg·mL-1. Correlation index (ρ) of cross-resistance level between flutolanil and thifluzamide, flutolanil and pencycuron, and thifluzamide and pencycuron was 0.398, 0.315, and 0.125, respectively. This is the first detailed study on AG identification, mycovirome analysis, and sensitivity to flutolanil, thifluzamide, and pencycuron of Rhizoctonia isolates associated with sugar beet root and crown rot.
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Affiliation(s)
- Can Zhao
- College of Plant Protection, China Agricultural University, Beijing 100193, China
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Siwei Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhihao Ma
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wenjun Wang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Lihong Gao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Anpei Yang
- Institute of Plant Protection, Xinjiang Academy of Agricultural Science, Urumqi 830091, China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
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12
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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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13
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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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14
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Ayllón MA, Vainio EJ. Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle. Adv Virus Res 2023; 115:1-86. [PMID: 37173063 DOI: 10.1016/bs.aivir.2023.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.
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Affiliation(s)
- María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain; Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
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15
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Lerer V, Shlezinger N. Inseparable companions: Fungal viruses as regulators of fungal fitness and host adaptation. Front Cell Infect Microbiol 2022; 12:1020608. [PMID: 36310864 PMCID: PMC9606465 DOI: 10.3389/fcimb.2022.1020608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/28/2022] [Indexed: 08/01/2023] Open
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16
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Chen X, Yu Z, Sun Y, Yang M, Jiang N. Molecular characterization of a novel partitivirus isolated from Rhizoctonia solani. Front Microbiol 2022; 13:978075. [PMID: 36204602 PMCID: PMC9531756 DOI: 10.3389/fmicb.2022.978075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Rhizoctonia solani is a widely distributed plant pathogen that can damage many crops. Here, we identified a novel mycovirus tentatively named Rhizoctonia solani partitivirus 433 (RsPV433) from an R. solani (AG-3) strain which caused tobacco target spot disease on flue-cured tobacco. RsPV433 was consisted of two dsRNA segments with lengths of 2450 and 2273 bp, which encoded an RNA-dependent RNA polymerase and a coat protein, respectively. BLASTP results of RsPV433 showed that the closest relative of RsPV433 was Sarcosphaera coronaria partitivirus (QLC36830.1), with an identity of 60.85% on the RdRp amino sequence. Phylogenetic analysis indicated that RsPV433 belonged to the Betapartitivirus genus in the Partitiviridae family. The virus transmission experiment revealed that RsPV433 can be transmitted horizontally. We further tested the biological effect of RsPV433 on R. solani strains and found that the RsPV433-infected R. solani strain grew slower than the RsPV433-free strain on the PDA medium and RsPV433 seemed to have no obvious impact on the lesion inducing ability of R. solani.
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Affiliation(s)
- Xiangru Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Zhaoyao Yu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Yujia Sun
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Meipeng Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Ning Jiang
- Agronomic Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
- *Correspondence: Ning Jiang
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17
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Khan HA, Telengech P, Kondo H, Bhatti MF, Suzuki N. Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan. Front Cell Infect Microbiol 2022; 12:913619. [PMID: 35846770 PMCID: PMC9277117 DOI: 10.3389/fcimb.2022.913619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/23/2022] Open
Abstract
Diplodia seriata in the family Botryosphaeriaceae is a cosmopolitan phytopathogenic fungus and is responsible for causing cankers, fruit rot and leaf spots on economically important plants. In this study, we characterized the virome of a single Pakistani strain (L3) of D. seriata. Several viral-like contig sequences were obtained via a previously conducted next-generation sequencing analysis. Multiple infection of the L3 strain by eight RNA mycoviruses was confirmed through RT-PCR using total RNA samples extracted from this strain; the entire genomes were determined via Sanger sequencing of RT-PCR and RACE clones. A BLAST search and phylogenetic analyses indicated that these eight mycoviruses belong to seven different viral families. Four identified mycoviruses belong to double-stranded RNA viral families, including Polymycoviridae, Chrysoviridae, Totiviridae and Partitiviridae, and the remaining four identified mycoviruses belong to single-stranded RNA viral families, i.e., Botourmiaviridae, and two previously proposed families "Ambiguiviridae" and "Splipalmiviridae". Of the eight, five mycoviruses appear to represent new virus species. A morphological comparison of L3 and partially cured strain L3ht1 suggested that one or more of the three viruses belonging to Polymycoviridae, "Splipalmiviridae" and "Ambiguiviridae" are involved in the irregular colony phenotype of L3. To our knowledge, this is the first report of diverse virome characterization from D. seriata.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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18
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Six Novel Mycoviruses Containing Positive Single-Stranded RNA and Double-Stranded RNA Genomes Co-Infect a Single Strain of the Rhizoctoniasolani AG-3 PT. Viruses 2022; 14:v14040813. [PMID: 35458543 PMCID: PMC9025235 DOI: 10.3390/v14040813] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 12/10/2022] Open
Abstract
Six novel mycoviruses that collectively represent the mycovirome of Rhizoctonia solani anastomosis group (AG)-3 PT strain ZJ-2H, which causes potato black scurf, were identified through metatranscriptome sequencing and putatively designated as Rhizoctonia solani fusarivirus 4 [RsFV4, positive single-stranded RNA (+ssRNA)], Rhizoctonia solani fusarivirus 5 (RsFV5, +ssRNA), Rhizoctonia solani mitovirus 40 (RsMV40, +ssRNA), Rhizoctonia solani partitivirus 10 [RsPV10, double-stranded RNA (dsRNA)], Rhizoctonia solani partitivirus 11 (RsPV11, dsRNA), and Rhizoctonia solani RNA virus 11 (RsRV11, dsRNA). Whole genome sequences of RsFV4, RsMV40, RsPV10, RsPV11, and RsRV11, as well as a partial genome sequence of RsFV5, were obtained. The 3'- and 5'- untranslated regions of the five mycoviruses with complete genome sequences were folded into stable stem-loop or panhandle secondary structures. RsFV4 and RsFV5 are most closely related to Rhizoctonia solani fusarivirus 1 (RsFV1), however, the first open reading frame (ORF) of RsFV4 and RsFV5 encode a hypothetical protein that differs from the first ORF of RsFV1, which encodes a helicase. We confirmed that RsPV10 and RsPV11 assemble into the spherical virus particles (approximately 30 nm in diameter) that were extracted from strain ZJ-2H. This is the first report that +ssRNA and dsRNA viruses co-infect a single strain of R. solani AG-3 PT.
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19
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Telengech P, Shahi S, Kondo H, Suzuki N. A novel deltapartitivirus from red clover. Arch Virol 2022; 167:1201-1204. [PMID: 35246731 DOI: 10.1007/s00705-022-05372-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/28/2022]
Abstract
The family Partitiviridae has five genera, among which is the genus Deltapartitivirus. We report here the complete genome sequence of a deltapartitivirus from red clover, termed "red clover cryptic virus 3" (RCCV3). RCCV3 has a bisegmented double-stranded (ds) RNA genome. dsRNA1 and dsRNA2 are 1580 and 1589 nucleotides (nt) in length and are predicted to encode an RNA-directed RNA polymerase (RdRP) and a capsid protein (CP), respectively. The RCCV3 RdRP shares the highest sequence identity with the RdRP of a previously reported deltapartitivirus, Medicago sativa deltapartitivirus 1 (MsDPV1) (76.5%), while the RCCV3 CP shows 50% sequence identity to the CP of MsDPV1. RdRP- and CP-based phylogenetic trees place RCCV3 into a clade of deltapartitiviruses. The sequence and phylogenetic analyses clearly indicate that RCCV3 represents a new species in the genus Deltapartitivirus. RCCV3 was detectable in all three tested cultivars of red clover.
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Affiliation(s)
- Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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20
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Wang S, Ahmed I, Li X, Nie J, Guo L. Evidence for a novel partitivirus isolated from the entomopathogenic nematode Steinernema ceratophorum. Arch Virol 2022; 167:969-972. [PMID: 35112200 DOI: 10.1007/s00705-021-05314-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Nematodes are abundant, but little is known about their viruses. In this study, we report a novel partitivirus isolated from the entomopathogenic nematode species Steinernema ceratophorum, named "Steinernema ceratophorum partitivirus 1" (ScPV-1). The complete genome of ScPV-1 comprises two dsRNA segments, dsRNA1 (2352 bp) and dsRNA2 (2196 bp). Each dsRNA contains a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. The sequences of the RdRp and CP showed the highest similarity (47% and 33% identity, respectively) to Plasmopara viticola associated partitivirus 7 (PvAP-7). A multiple sequence alignment and phylogenetic analysis of the RdRp of ScPV-1 and other selected viruses indicated that ScPV-1 is a new member of the genus Betapartitivirus in the family Partitiviridae.
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Affiliation(s)
- Shuangchao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Irfan Ahmed
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianhui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Nie
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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21
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Complete genome sequence of a novel partitivirus infecting the phytopathogenic fungus Alternaria tenuissima. Arch Virol 2022; 167:635-639. [PMID: 35031860 DOI: 10.1007/s00705-021-05332-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/30/2021] [Indexed: 11/02/2022]
Abstract
In the present study, a novel double-stranded RNA (dsRNA) mycovirus designated as "Alternaria tenuissima partitivirus 2" (AttPV2), was isolated from Alternaria tenuissima strain BJ-SY-1, a phytopathogenic fungus causing muskmelon leaf blight in Beijing municipality of China. The genome of AttPV2 comprises two dsRNA segments. The larger segment is 1829 bp in length and has a single open reading frame (ORF), potentially encoding a 65.8-kDa RNA-dependent RNA polymerase (RdRp), and the smaller segment is 1681 bp in length and also contains a single ORF, encoding a putative coat protein (CP) with a molecular mass of 56.0 kDa. BLASTp analysis revealed that the RdRp and CP encoded by the two ORFs of AttPV2 have the highest sequence identity, 85.9% and 75.0%, respectively, to their counterparts in Colletotrichum eremochloae partitivirus 1 (CePV1). Phylogenetic analysis based on RdRp sequences showed that AttPV2 clustered most closely with CePV1, a member of the proposed genus "Epsilonpartitivirus" in the family Partitiviridae. Hence, we propose that AttPV2 is a new epsilonpartitivirus from A. tenuissima. To the best of our knowledge, this is the first report of an epsilonpartitivirus infecting A. tenuissima.
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22
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Khan HA, Shamsi W, Jamal A, Javaied M, Sadiq M, Fatma T, Ahmed A, Arshad M, Waseem M, Babar S, Dogar MM, Virk N, Janjua HA, Kondo H, Suzuki N, Bhatti MF. Assessment of mycoviral diversity in Pakistani fungal isolates revealed infection by 11 novel viruses of a single strain of Fusarium mangiferae isolate SP1. J Gen Virol 2021; 102. [PMID: 34850675 DOI: 10.1099/jgv.0.001690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Wajeeha Shamsi
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Memoona Javaied
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mashal Sadiq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Maleeha Arshad
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mubashra Waseem
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Samra Babar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Midhat Mustafa Dogar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: EBS Universität für Wirtschaft und Recht, EBS Business School, Rheingaustrasse 1, 65375, Oestrich-Winkel, Germany
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
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23
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Sahin E, Keskin E, Akata I. Molecular characterization of the complete genome of a novel partitivirus hosted by the saprobic mushroom Leucocybe candicans. Arch Microbiol 2021; 203:5825-5830. [PMID: 34427724 DOI: 10.1007/s00203-021-02540-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/30/2021] [Accepted: 08/18/2021] [Indexed: 12/29/2022]
Abstract
Virus communities of uncultivated fungi stay largely unknown. In the current study, we characterized a new partitivirus species detected in the basidiomycetous, saprobic mushroom Leucocybe candicans, named "Leucocybe candicans partitivirus 1" (LcPV1). The full-length genome of LcPV1, determined using deep sequencing and RLM-RACE approaches, consists of two dsRNA segments with each having the same size of 1984 bp. Both dsRNA genome segments comprise a single open reading frame (ORF), encoding an RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. Based on BLASTp search, the sequences of the RdRp and CP show the highest identity (50.09% and 35.71% similarity, respectively) to those of partitiviruses reported from an oomycetous, plant pathogenic, stramenopile algae Plasmopara viticola and basidiomycetous, plant pathogenic fungus Ceratobasidium sp., respectively. Phylogenetic analyses performed based on the RdRp and CP sequences revealed that LcPV1 falls within a cluster that includes different alphapartitivirus species from the family Partitiviridae. In this study, we propose that LcPV1 is a new member of a species belonging to the genus Alphapartitivirus. To our knowledge, this is the first study reporting on a new fungal virus (mycovirus) identified in the basidiomycetous, saprobic mushroom Leucocybe candicans.
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Affiliation(s)
- Ergin Sahin
- Faculty of Science Department of Biology, Ankara University, 06100, Ankara, Tandogan, Turkey.
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, 06110, Ankara, Dışkapı, Turkey
| | - Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, 06100, Ankara, Tandogan, Turkey
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24
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Zhu JZ, Guo J, Hu Z, Zhang XT, Li XG, Zhong J. A Novel Partitivirus That Confer Hypovirulence to the Plant Pathogenic Fungus Colletotrichum liriopes. Front Microbiol 2021; 12:653809. [PMID: 34248869 PMCID: PMC8262616 DOI: 10.3389/fmicb.2021.653809] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022] Open
Abstract
Here, we report a novel double-stranded RNA virus designated Colletotrichum liriopes partitivirus 1 (ClPV1) from the plant pathogenic fungus C. liriopes. ClPV1 genome has two double stranded RNAs (dsRNAs), named as dsRNA 1 and dsRNA 2, which in the lengths of 1,807 and 1,706 bp, respectively. The dsRNA 1 and dsRNA 2 encoded proteins showing significant amino acid (aa) sequence identity to the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) of partitiviruses, respectively. Phylogenetic analysis using the aa sequences of RdRp and CP indicated that ClPV1 was grouped to members of the putative Epsilonpartitivirus genus in the Partitiviridae family. Spherical viral particles in approximately 35 nm in diameter and packaging the ClPV1 genome were isolated. Virus elimination and virus transfection with purified viral particles, and biological comparison revealed that ClPV1 could reduce the virulence and conidia production of C. liriopes. To the best of our knowledge, this is the first report of mycovirus in C. liriopes fungus.
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Affiliation(s)
- Jun Zi Zhu
- Hunan Engineering Research Center of Agricultural Pest Early Warning and Control, Hunan Agricultural University, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Jun Guo
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Zhao Hu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Xu Tong Zhang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Xiao Gang Li
- Hunan Engineering Research Center of Agricultural Pest Early Warning and Control, Hunan Agricultural University, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
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25
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Zhong J, Yang ZZ, Yang X, Guo ZJ, Xie W, Zhang YJ. Molecular characterization of a novel partitivirus and a fusarivirus coinfecting the fungus Nigrospora sphaerica. Arch Virol 2021; 166:2325-2331. [PMID: 34057607 DOI: 10.1007/s00705-021-05095-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
In this report, we describe the molecular characterization of two novel mycoviruses coinfecting the plant pathogenic fungus Nigrospora sphaerica, which were designated "Nigrospora sphaerica fusarivirus 1" (NsFV1) and "Nigrospora sphaerica partitivirus 1" (NsPV1). NsFV1 has an undivided genome measuring 6,147 nt, excluding the polyA tail, and was predicted to contain two nonoverlapping open reading frames (ORF1 and 2). The larger ORF1 encodes a polyprotein containing a conserved RNA-dependent RNA polymerase (RdRp) and a helicase domain that has functions related to RNA replication, and the smaller ORF2 encodes a putative protein with an unknown function. NsPV1 consists of two genome segments, which measure 1,796 bp and 1,455 bp in length. Each of the two dsRNAs has a single ORF, and they are predicted to encode proteins with homology to viral RdRps and coat proteins of members of the family Partitiviridae. Phylogenetic analysis indicated that NsFV1 is a member of the recently proposed family "Fusariviridae", while NsPV1 was determined to belong to the genus Gammapartitivirus in the family Partitiviridae. To the best of our knowledge, this report is the first to describe mycoviruses infecting N. sphaerica.
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Affiliation(s)
- Jie Zhong
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha City, Hunan Province, 410128, People's Republic of China
| | - Ze Zhong Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhao Jiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - You Jun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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26
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Sahin E, Keskin E, Akata I. Molecular characterization of a novel partitivirus hosted by the false morel mushroom Gyromitra esculenta. Arch Virol 2021; 166:1247-1251. [PMID: 33575894 DOI: 10.1007/s00705-021-04978-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Virus populations of uncultivated fungi remain scarcely studied. In the present study, we characterized a new partitivirus isolated from the false morel mushroom Gyromitra esculenta, named "Gyromitra esculenta partitivirus 1" (GePV1). The complete genome of GePV1, whose sequence was determined by combining high-throughput sequencing and RLM-RACE approaches, comprises two dsRNA segments of 1971 bp and 1799 bp, respectively. Each dsRNA genome segment contains a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a capsid protein (CP), respectively. The sequences of the RdRp and CP exhibited the highest similarity (69.77% and 47.00% identity, respectively) to those of Rosellinia necatrix partitivirus 2 (RnPV2). Phylogenetic analysis based on the CP and RdRp sequences demonstrated that GePV1 clusters within a clade that includes members of the genus Alphapartitivirus, family Partitiviridae. We propose that GePV1 is a new member of the genus Alphapartitivirus. This is the first study reporting on a new partitivirus identified in the false morel mushroom Gyromitra esculenta.
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Affiliation(s)
- Ergin Sahin
- Faculty of Science Department of Biology, Ankara University, 06100, Tandogan, Ankara, Turkey.
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, 06110, Dışkapı, Ankara, Turkey
| | - Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, 06100, Tandogan, Ankara, Turkey
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27
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Wan X, Zhao Y, Zhang Y, Wei C, Du H, Zhang H, Chen J, Yang L, Zang R, Wen C. Molecular characterization of a novel partitivirus isolated from the phytopathogenic fungus Aplosporella javeedii. Arch Virol 2021; 166:1237-1240. [PMID: 33560459 DOI: 10.1007/s00705-021-04988-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022]
Abstract
Aplosporella javeedii is a pathogenic fungus that causes canker and dieback of jujube in China. In this study, we report a new mycovirus, Aplosporella javeedii partitivirus 1 (AjPV1), isolated from A. javeedii strain NX55-3. The AjPV1 genome contains two double-stranded RNA elements (dsRNA1 and dsRNA2). The size of dsRNA1 is 2,360 bp, and it encodes a putative RNA-dependent RNA polymerase (RdRp), while dsRNA2 is 2,301 bp in length and encodes a putative capsid protein (CP). The sequences of RdRp and CP have significant similarity to those of members of the family Partitiviridae. Sequence alignment and phylogenetic analysis showed that AjPV1 is a new member of the family Partitiviridae that is related to members of the genus Betapartitivirus. To our knowledge, AjPV1 is the first mycovirus reported from A. javeedii.
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Affiliation(s)
- Xinru Wan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ying Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuanyuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Chenxing Wei
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Han Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Jiahui Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Lijie Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Rui Zang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Caiyi Wen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.
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28
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A novel mycovirus infecting Aspergillus nidulans that is closely related to viruses in a new genus of the family Partitiviridae. Arch Virol 2021; 166:659-664. [PMID: 33404858 DOI: 10.1007/s00705-020-04930-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022]
Abstract
The bisegmented genome of a novel double-stranded (ds) RNA mycovirus, named "Aspergillus nidulans partitivirus 1" (AnPV1), isolated from the fungus Aspergillus nidulans strain HJ5-47, was sequenced and analyzed. AnPV1 contains two segments, AnPV1-1 and AnPV1-2. AnPV1-1 has 1837 bp with an open reading frame (ORF) that potentially encodes a putative RNA-dependent RNA polymerase (RdRp) of 572 amino acids (aa). AnPV1-2 has 1583 bp with an ORF encoding a putative capsid protein (CP) of 488 aa. Phylogenetic analyses indicated that AnPV1 and related viruses clustered in a group that could represent a new unclassified genus in the family Partitiviridae.
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29
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Sahin E, Akata I. Full-length genome characterization of a novel alphapartitivirus detected in the ectomycorrhizal fungus Hygrophorus penarioides. Virus Genes 2021; 57:94-99. [PMID: 33392985 DOI: 10.1007/s11262-020-01814-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/17/2020] [Indexed: 12/25/2022]
Abstract
Virus populations of ectomycorrhizal fungi remain poorly studied. In the present study, we characterized a new partitivirus isolated from the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides, named "Hygrophorus penarioides partitivirus 1" (HpPV1). The whole genome of HpPV1, determined by merging deep sequencing and RLM-RACE approaches, comprised two dsRNA segments of 2053 bp and 2072 bp, respectively. Both dsRNA genome segments included a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. Based on BLASTp search, the sequences of the RdRp and CP exhibits the highest similarity (67.49% and 75.61% identity, respectively) to those of partitiviruses identified from an ascomycetous ectomycorrhizal fungus Sarcosphaera coronaria. Phylogenetic analyses performed based on the CP and RdRp sequences demonstrated that HpPV1 clusters within a clade that includes members of the genus Alphapartitivirus, belonging to the family Partitiviridae. Here, we propose that HpPV1 is a new member of the genus Alphapartitivirus. This is the first study reporting on a new partitivirus identified from the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides.
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Affiliation(s)
- Ergin Sahin
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey.
| | - Ilgaz Akata
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey
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30
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Virome characterization of Cryphonectria parasitica isolates from Azerbaijan unveiled a new mymonavirus and a putative new RNA virus unrelated to described viral sequences. Virology 2020; 553:51-61. [PMID: 33221630 DOI: 10.1016/j.virol.2020.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 11/24/2022]
Abstract
Cryphonectria parasitica, the causal agent of chestnut blight is controlled in Europe through natural spread of Cryphonectria hypovirus 1 (CHV1), a mycovirus able to induce hypovirulence to the host. In recent years C. parasitica was reported infecting Azerbaijani population of chestnut, but the presence of CHV1 still needs to be confirmed. Aim of this work was to investigate fifty-five C. parasitica isolates collected in Azerbaijan to describe the associated viruses. Our work found i) the first negative-sense ssRNA virus known to infect C. parasitica naturally for which we propose the name Cryphonectria parasitica sclerotimonavirus 1 (CpSV1) and ii) an RNA sequence showing peculiar features suggesting a viral nature for which we propose the name Cryphonectria parasitica ambivirus 1 (CpaV1). The discovery of CpaV1 expands our knowledge of the RNA virosphere suggesting the existence of a new lineage that cannot presently be reliably associated to the monophyletic Riboviria.
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31
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Ahmed I, Li P, Zhang L, Jiang X, Bhattacharjee P, Guo L, Wang S. First report of a novel partitivirus from the phytopathogenic fungus Fusarium cerealis in China. Arch Virol 2020; 165:2979-2983. [DOI: 10.1007/s00705-020-04802-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/08/2020] [Indexed: 12/16/2022]
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32
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Telengech P, Hisano S, Mugambi C, Hyodo K, Arjona-López JM, López-Herrera CJ, Kanematsu S, Kondo H, Suzuki N. Diverse Partitiviruses From the Phytopathogenic Fungus, Rosellinia necatrix. Front Microbiol 2020; 11:1064. [PMID: 32670213 PMCID: PMC7332551 DOI: 10.3389/fmicb.2020.01064] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/29/2020] [Indexed: 01/18/2023] Open
Abstract
Partitiviruses (dsRNA viruses, family Partitiviridae) are ubiquitously detected in plants and fungi. Although previous surveys suggested their omnipresence in the white root rot fungus, Rosellinia necatrix, only a few of them have been molecularly and biologically characterized thus far. We report the characterization of a total of 20 partitiviruses from 16 R. necatrix strains belonging to 15 new species, for which “Rosellinia necatrix partitivirus 11–Rosellinia necatrix partitivirus 25” were proposed, and 5 previously reported species. The newly identified partitiviruses have been taxonomically placed in two genera, Alphapartitivirus, and Betapartitivirus. Some partitiviruses were transfected into reference strains of the natural host, R. necatrix, and an experimental host, Cryphonectria parasitica, using purified virions. A comparative analysis of resultant transfectants revealed interesting differences and similarities between the RNA accumulation and symptom induction patterns of R. necatrix and C. parasitica. Other interesting findings include the identification of a probable reassortment event and a quintuple partitivirus infection of a single fungal strain. These combined results provide a foundation for further studies aimed at elucidating mechanisms that underly the differences observed.
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Affiliation(s)
- Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Cyrus Mugambi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Juan Manuel Arjona-López
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.,Institute for Sustainable Agriculture, Spanish Research Council, Córdoba, Spain
| | | | - Satoko Kanematsu
- Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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33
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Molecular characterization of a new partitivirus, MbPV1, isolated from the entomopathogenic fungus Metarhizium brunneum in China. Arch Virol 2020; 165:765-769. [PMID: 31894416 DOI: 10.1007/s00705-019-04517-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022]
Abstract
Mycoviruses from Metarhizium anisopliae have been extensively studied, but their sequences have yet to be deposited in the NCBI database. In the present study, we characterized a new partitivirus obtained from the entomogenous fungus Metarhizium brunneum, named "Metarhizium brunneum partitivirus 1" (MbPV1). The complete genome of MbPV1, determined by metagenomic sequencing, RT-PCR, and RACE, comprised two dsRNA segments of 1,829 bp and 1,720 bp, respectively. Both dsRNAs contained a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. The sequences of the RdRp and CP showed the highest similarity (61.4% and 44.4% identity, respectively) to those of Colletotrichum eremochloae partitivirus 1 (CePV1), which were obtained from the NCBI database. A phylogenetic tree based on the RdRp sequence showed that MbPV1 clustered with members of the proposed genus "Epsilonpartitivirus", belonging to family Partitiviridae. Here, we propose that MbPV1 is a member of a new species of the proposed genus "Epsilonpartitivirus". This is the first sequence data report of a new mycovirus from a member of the genus Metarhizium.
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34
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Complete genome sequence of a novel partitivirus from the entomogenous fungus Beauveria bassiana in China. Arch Virol 2019; 164:3141-3144. [DOI: 10.1007/s00705-019-04428-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/10/2019] [Indexed: 11/25/2022]
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35
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Nerva L, Forgia M, Ciuffo M, Chitarra W, Chiapello M, Vallino M, Varese GC, Turina M. The mycovirome of a fungal collection from the sea cucumber Holothuria polii. Virus Res 2019; 273:197737. [PMID: 31479695 DOI: 10.1016/j.virusres.2019.197737] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/11/2023]
Abstract
Holothuria polii is a marine animal with an important ecological and economic impact. In the present study we analysed the presence of mycoviruses associated to fungi that were isolated from different H. polii tissues. Among the 48 fungal isolates analysed we identified 10 viruses in 8 strains belonging to 7 fungal species. Five out of nine viruses have a dsRNA genome: three of them belong to the Partitiviridae family, one belongs to a still undefined clade of bipartite viruses and the last one belongs to the Chrysoviridae family. We also identified two viruses belonging to a recently proposed new mycovirus taxon named polymycovirus. Two viruses belong to the positive single stranded RNA clade: one falls into the new Botourmiaviridae family, specifically in the Magoulivirus genus, and the other one falls into a still undefined clade phylogenetically related to tombusviruses. Finally, we also identified a virus with a negative stranded RNA genome showing similarity to a group of viruses recently proposed as a new family of mycoviruses in the order Bunyavirales. A bioinformatics approach comparing two datasets of contigs containing two closely related mycobunyaviruses allowed us to identify putative nucleocapsids (Nc) and non-structural (Ns) associated proteins. The GenBank/eMBL/DDBJ accession numbers of the sequences reported in this paper are: PRJNA432529, MG913290, MG913291, MG887747, MG887748, MG887749, MG887750, MG887751, MG887752, MG887753, MG887754, MG887755, MG887756, MG887757, MG887758, MG887759, MG887760, MG887761, MG887762, MG887763, MG887764, MG887765, MG887766, MG887767, MH271211, MN163273, MN163274.
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Affiliation(s)
- L Nerva
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Research Centre for Viticulture and Enology, CREA, Via XXVIII Aprile 26, 31015 Conegliano, Italy
| | - M Forgia
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Mycotheca Universitatis Taurinensis (MUT), Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Torino, Italy
| | - M Ciuffo
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - W Chitarra
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Research Centre for Viticulture and Enology, CREA, Via XXVIII Aprile 26, 31015 Conegliano, Italy
| | - M Chiapello
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - M Vallino
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - G C Varese
- Mycotheca Universitatis Taurinensis (MUT), Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Torino, Italy
| | - M Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
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36
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Zhang T, Li N, Yuan Y, Cao Q, Chen Y, Tan B, Li G, Liu D. Blue-White Colony Selection of Virus-Infected Isogenic Recipients Based on a Chrysovirus Isolated from Penicillium italicum. Virol Sin 2019; 34:688-700. [PMID: 31376081 DOI: 10.1007/s12250-019-00150-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 05/14/2019] [Indexed: 11/29/2022] Open
Abstract
Mycoviruses have been found to infect more than 12 species of Penicillium, but have not been isolated from Penicillium italicum (P. italicum). In this study, we isolated and characterized a new double-stranded RNA (dsRNA) virus, designated Penicillium italicum chrysovirus 1 (PiCV1), from the citrus pathogen P. italicum HSPi-YN1. Viral genome sequencing and molecular characterization indicated that PiCV1 was highly homologous to the previously described Penicillium chrysogenum virus. We further constructed the mutant HSPi-YN1ΔpksP defective in the polyketide synthase gene (pksP), which is involved in pigment biosynthesis, and these mutants formed albino (white) colonies. Then we applied hyphal anastomosis method to horizontally transmit PiCV1 from the white virus-donors (i.e., HSPi-YN1 mutants) to wild-type recipients (i.e., P. italicum strains HSPi-CQ54, HSPi-HB4, and HSPi-HN1), and the desirable PiCV1-infected isogenic recipients, a certain part of blue wild-type strains, can be eventually selected and confirmed by viral genomic dsRNA profile analysis. This blue-white colony screening would be an easier method to select virus-infected P. italicum recipients, according to distinguishable color phenotypes between blue virus-recipients and white virus-donors. In summary, the current work newly isolated and characterized PiCV1, verified its horizontal transmission among dually cultured P. italicum isolates, and based on these, established an effective and simplified approach to screen PiCV1-infected isogenic recipients.
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Affiliation(s)
- Tingfu Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Na Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.,Yunnan Higher Education Institutions, College of Life Science and Technology, Honghe University, Mengzi, 661199, China
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Qianwen Cao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yanfen Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Binglan Tan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Guoqi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
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37
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Vuković R, Liber Z, Ježić M, Sotirovski K, Ćurković-Perica M. Link between epigenetic diversity and invasive status of south-eastern European populations of phytopathogenic fungus Cryphonectria parasitica. Environ Microbiol 2019; 21:4521-4536. [PMID: 31314941 DOI: 10.1111/1462-2920.14742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Epigenetic modifications may play an important role in invasion and adaptation of clonal and invasive populations to different environments. The aim of this study was to analyse epigenetic diversity and structure within and among populations of invasive pathogenic fungus Cryphonectria parasitica from south-eastern Europe, where one haplotype S12 dominates. The highest level of epigenetic diversity was found in haplotype S1, followed by S2, while the lowest level of epigenetic diversity was found in haplotype S12. Similar pattern of epigenetic diversity was detected in the control, genetically diverse Croatian population where S1 haplotype dominates. In four south-eastern European populations, the highest level of epigenetic diversity was observed in the Italian population, the oldest population in the studied area, while the lowest diversity was found in most recently established Bulgarian population. This relationship between epigenetic diversity and population age implies the important role of epigenetic modifications on the process of invasion. Our data suggest that epigenetic differences might affect the success of expansion of certain haplotype into new regions. Understanding the role of epigenetic processes in expansion and (pre)adaptation of fungal plant pathogens, besides fundamental knowledge, can contribute to development of strategies for control of fungal spread and pathogenesis.
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Affiliation(s)
- Rosemary Vuković
- Department of Biology, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Zlatko Liber
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Kiril Sotirovski
- Faculty of Forestry, Ss. Cyril and Methodius University of Skopje, Skopje, North Macedonia
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38
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Gilbert KB, Holcomb EE, Allscheid RL, Carrington JC. Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes. PLoS One 2019; 14:e0219207. [PMID: 31339899 PMCID: PMC6655640 DOI: 10.1371/journal.pone.0219207] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/18/2019] [Indexed: 11/25/2022] Open
Abstract
The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
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Affiliation(s)
- Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Emily E. Holcomb
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Robyn L. Allscheid
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - James C. Carrington
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
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39
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Picarelli MASC, Forgia M, Rivas EB, Nerva L, Chiapello M, Turina M, Colariccio A. Extreme Diversity of Mycoviruses Present in Isolates of Rhizoctonia solani AG2-2 LP From Zoysia japonica From Brazil. Front Cell Infect Microbiol 2019; 9:244. [PMID: 31355150 PMCID: PMC6640214 DOI: 10.3389/fcimb.2019.00244] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 11/16/2022] Open
Abstract
Zoysia japonica, in Brazil, is commonly infected by Rhizoctonia solani (R. solani) in humid and cool weather conditions. Eight isolates of R. solani, previously identified as belonging to the AG2-2 LP anastomosis group, isolated from samples from large path symptoms, were collected from three counties in São Paulo state (Brazil) and investigated for the presence of mycoviruses. After detection of double-strand RNA (dsRNA) in all samples, RNA_Seq analysis of ribosomal RNA-depleted total RNA from in vitro cultivated mycelia was performed. Forty-seven partial or complete viral unique RNA dependent-RNA polymerase (RdRp) sequences were obtained with a high prevalence of positive sense ssRNA viruses. Sequences were sufficiently different from the first match in BLAST searches suggesting that they all qualify as possible new viral species, except for one sequence showing an almost complete match with Rhizoctonia solani dsRNA virus 2, an alphapartitivirus. Surprisingly four large contigs of putative viral RNA could not be assigned to any existing clade of viruses present in the databases, but no DNA was detected corresponding to these fragments confirming their viral replicative nature. This is the first report on the occurrence of mycoviruses in R. solani AG2-2 LP in South America.
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Affiliation(s)
| | - Marco Forgia
- Department of Life Science and System Biology, University of Turin, Turin, Italy.,Institute for Sustainable Plant Protection, CNR, Turin, Italy
| | - Eliana B Rivas
- Phytopathological Diagnostic Laboratory, Instituto Biológico, São Paulo, Brazil
| | - Luca Nerva
- Institute for Sustainable Plant Protection, CNR, Turin, Italy.,Council for Agricultural Research and Economics-Research Centre for Viticulture and Enology CREA-VE, Conegliano, Italy
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
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40
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Komatsu A, Kondo H, Sato M, Kurahashi A, Nishibori K, Suzuki N, Fujimori F. Isolation and characterization of a novel mycovirus infecting an edible mushroom, Grifola frondosa. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Nerva L, Turina M, Zanzotto A, Gardiman M, Gaiotti F, Gambino G, Chitarra W. Isolation, molecular characterization and virome analysis of culturable wood fungal endophytes in esca symptomatic and asymptomatic grapevine plants. Environ Microbiol 2019; 21:2886-2904. [DOI: 10.1111/1462-2920.14651] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Luca Nerva
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
| | - Alessandro Zanzotto
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
| | - Massimo Gardiman
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
| | - Federica Gaiotti
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
| | - Walter Chitarra
- Council for Agricultural Research and Economics – Research Centre for Viticulture and Enology CREA‐VE Via XXVIII Aprile 26, 31015 Conegliano (TV) Italy
- Institute for Sustainable Plant Protection CNR, Strada delle Cacce 73, 10135 Torino Italy
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42
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Jiang Y, Wang J, Yang B, Wang Q, Zhou J, Yu W. Molecular Characterization of a Debilitation-Associated Partitivirus Infecting the Pathogenic Fungus Aspergillus flavus. Front Microbiol 2019; 10:626. [PMID: 30984147 PMCID: PMC6447663 DOI: 10.3389/fmicb.2019.00626] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/12/2019] [Indexed: 12/17/2022] Open
Abstract
The opportunistic human pathogenic fungus Aspergillus flavus is known to be infected with mycoviruses. In this study, we report a novel mycovirus A. flavus partitivirus 1 (AfPV1) that was originally isolated from the abnormal colonial morphology isolate LD-3-8 of A. flavus. AfPV1 has spherical virus-like particles about 40 nm in diameter, and three double-stranded RNA (dsRNA) segments (dsRNA1, 2, and 3 with lengths of 1.7, 1.4, and 1.1 kbp, respectively) were packaged in the virions. dsRNA1, dsRNA2, and dsRNA3 each contained a single open reading frame and potentially encoded 62, 42, and 32 kDa proteins, respectively. The dsRNA1 encoded protein shows similarity to the RNA-dependent RNA polymerase (RdRp) of partitiviruses, and the dsRNA2 product has no significant similarity to any other capsid protein (CP) in the GenBank databases, beside some homology with the hypothetical "capsid" protein of a few partitiviruses. The dsRNA3 encodes a protein with no similarity to any protein in the GenBank database. SDS-PAGE and polypeptide mass fingerprint-mass spectrum (PMF-MS) analyses indicated that the CP of the AfPV1 was encoded by dsRNA2. Phylogenetic analysis showed that the AfPV1 and relative viruses were found in an unclassified group inside the Partitiviridae family. AfPV1 seems to result in debilitation symptoms, but had no significant effects to murine pathogenicity. These findings provide new insights into the partitiviruses taxonomy and the interactions between viruses and A. flavus.
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Affiliation(s)
- Yinhui Jiang
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Jingxian Wang
- Experiment Center of Stem Cell and Tissue Engineering Research, Guizhou Medical University, Guiyang, China
| | - Bi Yang
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Jianjiang Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
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43
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Nerva L, Chitarra W, Siciliano I, Gaiotti F, Ciuffo M, Forgia M, Varese GC, Turina M. Mycoviruses mediate mycotoxin regulation in Aspergillus ochraceus. Environ Microbiol 2018; 21:1957-1968. [PMID: 30289193 DOI: 10.1111/1462-2920.14436] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/24/2018] [Accepted: 09/27/2018] [Indexed: 12/30/2022]
Abstract
To date, no demonstration of a direct correlation between the presence of mycoviruses and the quantitative or qualitative modulation of mycotoxins has been shown. In our study, we transfected a virus-free ochratoxin A (OTA)-producing isolate of Aspergillus ochraceus with purified mycoviruses from a different A. ochraceus isolate and from Penicillium aurantiogriseum. Among the mycoviruses tested, only Aspergillus ochraceus virus (AoV), a partitivirus widespread in A. ochraceus, caused a specific interaction that led to an overproduction of OTA, which is regulated by the European Commission and is the second most important contaminant of food and feed commodities. Gene expression analysis failed to reveal a specific viral upregulation of the mRNA of genes considered to play a role in the OTA biosynthetic pathway. Furthermore, AoOTApks1, a polyketide synthase gene considered essential for OTA production, is surprisingly absent in the genome of our OTA-producing isolate. The possible biological and evolutionary implications of the mycoviral regulation of mycotoxin production are discussed.
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Affiliation(s)
- L Nerva
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015, Conegliano (TV), Italy.,Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - W Chitarra
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015, Conegliano (TV), Italy.,Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - I Siciliano
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015, Conegliano (TV), Italy
| | - F Gaiotti
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015, Conegliano (TV), Italy
| | - M Ciuffo
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - M Forgia
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135, Torino, Italy.,Mycotheca Universitatis Taurinensis (MUT), Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - G C Varese
- Mycotheca Universitatis Taurinensis (MUT), Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125, Torino, Italy
| | - M Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135, Torino, Italy
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44
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Turina M, Ghignone S, Astolfi N, Silvestri A, Bonfante P, Lanfranco L. The virome of the arbuscular mycorrhizal fungus
Gigaspora margarita
reveals the first report of DNA fragments corresponding to replicating non‐retroviral RNA viruses in fungi. Environ Microbiol 2018; 20:2012-2025. [DOI: 10.1111/1462-2920.14060] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/23/2018] [Accepted: 01/28/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Massimo Turina
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 7310131 Torino Italy
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 7310131 Torino Italy
| | - Nausicaa Astolfi
- Department of Life Sciences and Systems BiologyUniversity of Torino, Viale P.A. Mattioli 2510125 Torino Italy
| | - Alessandro Silvestri
- Department of Life Sciences and Systems BiologyUniversity of Torino, Viale P.A. Mattioli 2510125 Torino Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems BiologyUniversity of Torino, Viale P.A. Mattioli 2510125 Torino Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems BiologyUniversity of Torino, Viale P.A. Mattioli 2510125 Torino Italy
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45
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Lyu R, Zhang Y, Tang Q, Li Y, Cheng J, Fu Y, Chen T, Jiang D, Xie J. Two alphapartitiviruses co-infecting a single isolate of the plant pathogenic fungus Rhizoctonia solani. Arch Virol 2017; 163:515-520. [PMID: 29101540 DOI: 10.1007/s00705-017-3627-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/25/2017] [Indexed: 11/24/2022]
Abstract
Seven dsRNA segments were detected from a single Rhizoctonia solani strain HG81. From the full-length cDNA sequences of four smaller dsRNA segments, the genomes of two related partitiviruses, designated as Rhizoctonia solani partitivirus 3 (RsPV3) and RsPV4, were determined. The genomes of RsPV3 and RsPV4 are both composed of two separate dsRNA segments, with each segment possessing a single open reading frame (ORF). ORF1 from RsPV3 and RsPV4 encodes a putative RNA-dependent RNA polymerase, while ORF2 of RsPV3 and RsPV4 encodes a putative capsid protein. RsPV3 and RsPV4 share high sequence identity with viruses classified within the genus Alphapartitivirus, family Partitiviridae.
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Affiliation(s)
- Ruiling Lyu
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yi Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qing Tang
- Xiangyang Academy of Agricultural Sciences, Xiangyang, 441057, Hubei, China
| | - Yangyi Li
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanping Fu
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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