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Zhao YJ, Hosoya T, Urayama S, Hagiwara D. Seven new mycoviruses identified from isolated ascomycetous macrofungi. Virus Res 2024; 339:199290. [PMID: 38043725 PMCID: PMC10751708 DOI: 10.1016/j.virusres.2023.199290] [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: 10/13/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Mycoviruses have been described in all major fungal taxonomic groups. There has been much focus on commercially cultivated basidiomycetous macrofungi, while attention to viruses from ascomycetous macrofungi is lacking. Therefore, in this study, we conducted viral screening against fungal mycelia that were regenerated from ascomycetous macrofungi using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 57 isolates, four isolates were detected with virus-like bands through screening with AGE, and subsequent FLDS analyses determined the viral sequences. Other isolates without virus-like bands in AGE were pooled to check for viral sequences. Using FLDS analysis, a total of seven new mycoviruses were identified, including two double-stranded RNA (dsRNA) viruses belonging to Quadriviridae and Partitiviridae, five positive-sense single-stranded RNA (ssRNA) viruses (three belonging to Mitoviridae, one belonging to Endornaviridae and one belonging to Virgaviridae). All viruses characterized in this study are novel species, and all the hosts are firstly reported to be infected by mycoviruses. These findings expand our knowledge of the diversity of mycoviruses from macrofungi in natural environments.
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Affiliation(s)
- Yan-Jie Zhao
- 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.
| | - Tsuyoshi Hosoya
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Syunichi Urayama
- 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; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Daisuke Hagiwara
- 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; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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Lopez-Jimenez J, Herrera J, Alzate JF. Expanding the knowledge frontier of mitoviruses in Cannabis sativa. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105523. [PMID: 37940011 DOI: 10.1016/j.meegid.2023.105523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/25/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within the Cannabaceae family. Cannabis sativa has been in the spotlight in recent years due to the growing industrial applications of plant derivatives, such as fiber and secondary metabolites. Given the importance of Cannabis in today's agriculture, our study aimed to expand the knowledge frontier of Mitoviruses in C. sativa by increasing the number of reference genomes of CasaMV1 available in public databases and representing a larger number of crops in countries where its industrial-scale growth is legalized. To achieve this goal, we used transcriptomics to sequence the first mitoviral genomes of Colombian crops and analyzed RNA-seq datasets available in the SRA databank. Additionally, the evolutionary analysis performed using the mitovirus genomes revealed two main lineages of CasaMV1, termed CasaMV1_L1 and CasaMV1_L2. These mitoviral lineages showed strong clustering based on the geographic location of the crops and differential expression intensities.
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Affiliation(s)
- Juliana Lopez-Jimenez
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Jorge Herrera
- Fábrica de Plantas y Semillas de Antioquia S.A.S. - FASPLAN, El Carmen de Viboral, Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia; Fábrica de Plantas y Semillas de Antioquia S.A.S. - FASPLAN, El Carmen de Viboral, Antioquia, Colombia; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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Wu Y, Liu L, Zhang M, Zhan H, Wang C, Wang M, Chen S, Jia R, Yang Q, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. A Recombinant Duck Plague Virus Containing the ICP27 Deletion Marker Provides Robust Protection in Ducks. Microbiol Spectr 2023; 11:e0098323. [PMID: 37404171 PMCID: PMC10434260 DOI: 10.1128/spectrum.00983-23] [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: 03/08/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Duck plague virus (DPV) is a member of Alphaherpesvirus genus and poses a major threat to waterfowl breeding. Genetic engineered vaccines that are capable of distinguishing naturally infected from vaccine-immunized animals are useful for eradicating duck plague. In this study, reverse genetics was used to develop an ICP27-deficient strain (CHv-ΔICP27), and its potential as a marker vaccination candidate was evaluated. The results showed that the CHv-ΔICP27 generated in this study exhibited good genetic stability in vitro and was highly attenuated both in vivo and in vitro. The level of neutralizing antibody generated by CHv-ΔICP27 was comparable to that induced by a commercial DPV vaccine, suggesting that it could protect ducks from virulent DPV attack. By using molecular identification techniques such as PCR, restriction fragment length polymorphism, immunofluorescence, Western blotting, and others, it is possible to differentiate the CHv-ΔICP27 from wild-type strains. Moreover, ICP27 can also be a potential target for the genetic engineering vaccine development of alphavirus or perhaps the entire herpesvirus family members due to the highly conservative of ICP27 protein in all herpesvirus family members. IMPORTANCE The development of distinguishable marker vaccines from natural infection is a key step toward eradicating duck plague. Here, we generated a recombinant DPV that carries an ICP27 deletion marker that could be easily distinguished from wild-type strain by molecular biological methods. It was highly attenuated in vitro and in vivo and could provide comparable protection to ducks after a single dose of immunizations, as commercial vaccines did. Our findings support the use of the ICP27-deficient virus as a marker vaccine for DPV control and future eradication.
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Affiliation(s)
- Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Lu Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Mengya Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Haichuan Zhan
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Chenjia Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Xinxin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Xumin Ou
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Sai Mao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Qun Gao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Di Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Bin Tian
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, People’s Republic of China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, People’s Republic of China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People’s Republic of China
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Hough B, Steenkamp E, Wingfield B, Read D. Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses. Viruses 2023; 15:1202. [PMID: 37243288 PMCID: PMC10224137 DOI: 10.3390/v15051202] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.
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Affiliation(s)
| | | | - Brenda Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria 0002, South Africa; (B.H.); (E.S.); (D.R.)
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Zhao YJ, Shirouzu T, Chiba Y, Hosaka K, Moriyama H, Urayama SI, Hagiwara D. Identification of novel RNA mycoviruses from wild mushroom isolates in Japan. Virus Res 2023; 325:199045. [PMID: 36681193 DOI: 10.1016/j.virusres.2023.199045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The characterization of viruses from environmental samples could aid in our understanding of their ecological significance and potential for biotechnological exploitation. While there has been much focus on pathogenic fungi or commercially cultivated mushrooms, attention to viruses from wild Basidiomycota mushrooms is lacking. Therefore, in this study, we conducted viral screening of fungal mycelia isolated from wild basidiocarps using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 51 isolates, seven isolates were detected with virus-like bands during the initial screening with AGE, but only five isolates were detected with viruses after long-term storage. Using the FLDS method, we obtained seven viral genome sequences, including five double-stranded RNA (dsRNA) viruses belonging to Partitiviridae and Curvulaviridae, one positive-sense single-stranded RNA (ssRNA) virus belonging to Endornaviridae and one negative-sense ssRNA virus belonging to Tulasviridae (Bunyavirales). All viruses characterized in this study are novel species. These findings greatly expanded our knowledge of the diversity of RNA viruses from environmental samples.
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Affiliation(s)
- Yan-Jie Zhao
- 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
| | - Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Yuto Chiba
- 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
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Syun-Ichi Urayama
- 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; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Daisuke Hagiwara
- 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; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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Abstract
Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus diversity and abundance in 1,079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analyzing open-source data from the 1000 Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% were single-stranded positive-sense RNA viruses across eight orders, including members of the Hepelivirales, Tymovirales, Cryppavirales, Martellivirales, and Picornavirales. One-third of the newly described viruses were double-stranded RNA viruses from the orders Durnavirales and Ghabrivirales. The remaining were negative-sense RNA viruses from the Rhabdoviridae, Aspiviridae, Yueviridae, and Phenuiviridae and the newly proposed Viridisbunyaviridae. Our analysis considerably expands the known host range of 13 virus families to include lower plants (e.g., Benyviridae and Secoviridae) and 4 virus families to include alga hosts (e.g., Tymoviridae and Chrysoviridae). More broadly, however, a cophylogeny analysis revealed that the evolutionary history of these families is largely driven by cross-species transmission events. The discovery of the first 30-kDa movement protein in a nonvascular plant suggests that the acquisition of plant virus movement proteins occurred prior to the emergence of the plant vascular system. Together, these data highlight that numerous RNA virus families are associated with older evolutionary plant lineages than previously thought and that the apparent scarcity of RNA viruses found in lower plants likely reflects a lack of investigation rather than their absence. IMPORTANCE Our knowledge of plant viruses is mainly limited to those infecting economically important host species. In particular, we know little about those viruses infecting basal plant lineages such as the ferns, lycophytes, bryophytes, and charophytes. To expand this understanding, we conducted a broad-scale viral survey of species across the breadth of the plant kingdom. We found that basal plants harbor a wide diversity of RNA viruses, including some that are sufficiently divergent to likely compose a new virus family. The basal plant virome revealed offers key insights into the evolutionary history of core plant virus gene modules and genome segments. More broadly, this work emphasizes that the scarcity of viruses found in these species to date most likely reflects the limited research in this area.
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Shamsi W, Kondo H, Ulrich S, Rigling D, Prospero S. Novel RNA viruses from the native range of Hymenoscyphus fraxineus, the causal fungal agent of ash dieback. Virus Res 2022; 320:198901. [PMID: 36058013 DOI: 10.1016/j.virusres.2022.198901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022]
Abstract
The native Japanese population of the fungus Hymenoscyphus fraxineus, the causal agent of ash dieback in Europe, was screened for viruses using a high-throughput sequencing method. Five RNA viruses were detected in 116 fungal isolates sequenced via Illumina RNA-seq platform, with an overall virus prevalence of 11.2%. The viruses were completely sequenced by RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) followed by Sanger sequencing. The sequences appear to represent new species from three established families (Mito-, Endorna- and Partitiviridae), one recognized genus (Botybirnavirus) and a negative-sense single-stranded RNA virus in the order Bunyavirales from the proposed family "Mybuviridae". The highest prevalence was found for the mitovirus (7.8%), that had two genomic forms (linear and circular), while the other viruses were detected each in one isolate. Co-infection of a mitovirus and an endornavirus was also observed in one of the infected isolates. Here we describe the molecular characterization of the identified viruses. This study expands the diversity of viruses in H. fraxineus and provides the basis for investigating the virus-mediated control of ash dieback in Europe.
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Affiliation(s)
- Wajeeha Shamsi
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Sven Ulrich
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Daniel Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
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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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9
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Vainio EJ. Mitoviruses in the conifer root rot pathogens Heterobasidion annosum and H. parviporum. Virus Res 2019; 271:197681. [PMID: 31394105 DOI: 10.1016/j.virusres.2019.197681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 10/26/2022]
Abstract
Mitoviral infections are highly common among fungi, but so far only one mitovirus has been described in Heterobasidion spp. conifer pathogens. Here, the occurrence of further mitoviruses was investigated using a previously published RNA-Seq dataset for de novo contig assembly. This allowed the identification of two additional mitovirus strains designated as Heterobasidion mitovirus 2 (HetMV2) and HetMV3 with genome lengths of ca. 2.9 and 5.0 kb. Furthermore, the occurrence of similar viruses was screened among a collection of Heterobasidion isolates using RT-PCR. Mitoviruses were detected in six more fungal isolates and two different host species, H. annosum and H. parviporum.
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Affiliation(s)
- Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland.
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10
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Sutela S, Poimala A, Vainio EJ. Viruses of fungi and oomycetes in the soil environment. FEMS Microbiol Ecol 2019; 95:5542194. [DOI: 10.1093/femsec/fiz119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACTSoils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus–host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.
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Affiliation(s)
- Suvi Sutela
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Anna Poimala
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
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11
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Nibert ML, Vong M, Fugate KK, Debat HJ. Evidence for contemporary plant mitoviruses. Virology 2018; 518:14-24. [PMID: 29438872 PMCID: PMC6668999 DOI: 10.1016/j.virol.2018.02.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/02/2018] [Accepted: 02/03/2018] [Indexed: 10/18/2022]
Abstract
Mitoviruses have small RNA(+) genomes, replicate in mitochondria, and have been shown to infect only fungi to date. For this report, sequences that appear to represent nearly complete plant mitovirus genomes were recovered from publicly available transcriptome data. Twenty of the refined sequences, 2684-2898 nt long and derived from 10 different species of land plants, appear to encompass the complete coding regions of contemporary plant mitoviruses, which furthermore constitute a monophyletic cluster within genus Mitovirus. Complete coding sequences of several of these viruses were recovered from multiple transcriptome (but not genome) studies of the same plant species and also from multiple plant tissues. Crop plants among implicated hosts include beet and hemp. Other new results suggest that such genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes. Whether these mitoviruses are wholly cryptic with regard to plant health remains to be investigated.
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Affiliation(s)
- Max L Nibert
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Minh Vong
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Karen K Fugate
- Sugarbeet and Potato Research, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Red River Valley Agricultural Research Center, Fargo, ND 58102, USA
| | - Humberto J Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), X5020ICA, Córdoba, Argentina
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12
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Sahin E, Akata I. Viruses infecting macrofungi. Virusdisease 2018; 29:1-18. [PMID: 29607353 DOI: 10.1007/s13337-018-0434-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/25/2018] [Indexed: 11/26/2022] Open
Abstract
Ever since their discovery just about 56 years ago in the cultivated mushroom Agaricus bisporus, many more viruses infecting fungi have been identified in a wide range of fungal taxa. With mostly being asymptomatic, especially the ones that are detrimental to their phytopathogenic hosts are intensively studied due to their considerable importance in developing novel plant protection measures. Contrary to the rapid accumulation of notable data on viruses of plant pathogenic microfungi, much less information have hitherto been obtained in regards to the viruses whose hosts are macrofungi. According to the current literature, only more than 80 distinct viruses bearing either linear dsRNA or linear positive sense ssRNA genome and infecting a total number of 34 macrofungal species represented with four Ascomycota and 30 Basidiomycota have been identified so far. Among these 34 macrofungal species, 14 are cultivated edible and wild edible mushroom species. According to the 10th ICTV (International Committee on Taxonomy of Viruses) Report, macrofungal viruses with linear dsRNA genome are classified into five families (Partitiviridae, Totiviridae, Chrysoviridae, Endornaviridae and Hypoviridae) and macrofungal viruses with linear positive sense ssRNA genome are classified into seven families (Betaflexiviridae, Gammaflexiviridae, Barnaviridae, Narnaviridae, Virgaviridae, Benyviridae and Tymoviridae). In this review, following a brief overview of some general characteristics of fungal viruses, an up to date knowledge on viruses infecting macrofungal hosts were presented by summarizing the previous, recent and prospective studies of the field.
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Affiliation(s)
- Ergin Sahin
- Faculty of Science, Department of Biology, Ankara University, Ankara, Turkey
| | - Ilgaz Akata
- Faculty of Science, Department of Biology, Ankara University, Ankara, Turkey
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13
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Mitovirus UGA(Trp) codon usage parallels that of host mitochondria. Virology 2017; 507:96-100. [PMID: 28431284 DOI: 10.1016/j.virol.2017.04.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 02/02/2023]
Abstract
Mitoviruses replicate in mitochondria of their host fungi. They have small RNA genomes that encompass a single ORF encoding the viral RdRp. Since UGA codons encode Trp in fungal mitochondria, the RdRp ORF of a typical mitovirus includes multiple UGA codons. In some mitoviruses, however, the ORF has no such codons, suggesting that these particular viruses may be under selective pressure to exclude them. In this report, new evidence is presented that host fungi whose mitoviruses have no or few UGA codons are distinctive in also having no or few UGA codons in their core mitochondrial genes. Thus, the relative exclusion of such codons in a subset of mitoviruses appears to reflect most fundamentally that UGA(Trp) is a rare mitochondrial codon in their particular hosts. The fact that UGA(Trp) is a rare mitochondrial codon in many fungi appears not to have been widely discussed to date.
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14
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Liu J, Zhang H, Zhao Y, Xia L, Guo C, Yang H, Luo N, He Z, Ma S. Characterization of four vaccine-related polioviruses including two intertypic type 3/type 2 recombinants associated with aseptic encephalitis. Virol J 2016; 13:162. [PMID: 27677968 PMCID: PMC5039789 DOI: 10.1186/s12985-016-0615-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/14/2016] [Indexed: 11/17/2022] Open
Abstract
Background Four vaccine-related polioviruses (VRPV) were isolated from aseptic encephalitis cases in Yunnan, China in 2010. The genomic sequences of these VRPVs were investigated to gain a better understanding of their molecular characteristics. Methods Molecular typing was performed by amplification and sequencing of the VP1 region. The genomic sequences of the four VRPV3 strains were compared to vaccine strain and wild strain sequences to study genetic drift and recombination. Results All four isolates could be entirely neutralized by polyclonal poliovirus 3 (PV3) antisera but not by PV1 and PV2 antisera and displayed a temperature-sensitive phenotype. The genomic sequences of all four isolates contained two Sabin 3-specific attenuating mutations at nucleotides 472(C → T) and 2034(C → T), but a third Sabin 3-specific attenuating mutation at position 2493 (T → C) had reverted back to a T. Recombination analyses showed RF108/YN/CHN/2010 and RF134/YN/CHN/2010 strain recombined with Sabin 2 at the 3′-end of the 2C to 3′-untranslated region (3′-UTR) and at the 5′-end of the 3D to 3′-UTR, respectively. Conclusion Four VRPV3 strains including two type 3/type 2 intertypic recombinants were identified. The recombination of Sabin vaccine strains with other Sabin serotypes or human enterovirus C species could be a critical factor in the potential of emerging viruses and related disease outbreaks. Therefore, it is essential to be persistent in the surveillance of EVs (including PV). Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0615-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiansheng Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Haihao Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Yilin Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Longhui Xia
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Chen Guo
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Huai Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Na Luo
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China.
| | - Shaohui Ma
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, Yunnan Province, 650118, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China.
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15
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Characterization of Five Novel Mitoviruses in the White Pine Blister Rust Fungus Cronartium ribicola. PLoS One 2016; 11:e0154267. [PMID: 27196406 PMCID: PMC4873031 DOI: 10.1371/journal.pone.0154267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022] Open
Abstract
The white pine blister rust (WPBR) fungus Cronartium ribicola (J.C. Fisch.) is an exotic invasive forest pathogen causing severe stem canker disease of native white pine trees (subgenus Strobus) in North America. The present study reports discovery of five novel mitoviruses in C. ribicola by deep RNA sequencing. The complete genome of each mitovirus was determined by rapid amplification of cDNA ends (RACE) and reverse transcriptase-polymerase chain reaction (RT-PCR). A single open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) was detected in each of the viral genomes using mitochondrial genetic codes. Phylogenetic analysis indicated that the C. ribicola mitoviruses (CrMV1 to CrMV5) are new putative species of the genus Mitovirus. qRT-PCR and RNA-Seq analyses revealed that viral RNAs were significantly increased in fungal mycelia in cankered pine stems compared to expression during two different stages of spore development, suggesting that viral genome replication and transcription benefit from active growth of the host fungus. CrMVs were widespread with relatively high levels of minor allele frequency (MAF) in western North America. As the first report of mitoviruses in the Class Pucciniomycetes, this work allows further investigation of the dynamics of a viral community in the WPBR pathosystem, including potential impacts that may affect pathogenicity and virulence of the host fungus.
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16
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Ratti C, Iotti M, Zambonelli A, Terlizzi F. Mycoviruses Infecting True Truffles. SOIL BIOLOGY 2016. [DOI: 10.1007/978-3-319-31436-5_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Vainio EJ, Hantula J. Taxonomy, biogeography and importance of Heterobasidion viruses. Virus Res 2015; 219:2-10. [PMID: 26477938 DOI: 10.1016/j.virusres.2015.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/08/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
The genus Heterobasidion consists of several species of necrotrophic and saprotrophic fungi, and includes some of the most detrimental organisms in boreal conifer forests. These fungi host a widespread and diverse mycovirus community composed of more than 16 species of Partitiviridae, a species of Narnaviridae and one taxonomically unassigned virus related to the Curvularia thermal tolerance virus. These viruses are able to cross species borders, co-infect single host strains and cause phenotypic changes in their hosts. The abundance of viruses increases over time in Heterobasidion infection centers, and they are targeted by fungal RNA interference. Long-term field studies are essential for obtaining a comprehensive view of virus effects in the nature.
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Affiliation(s)
- Eeva J Vainio
- Natural Resources Institute Finland (Luke), Jokiniemenkuja 1, POB 18, 01301 Vantaa, Finland.
| | - Jarkko Hantula
- Natural Resources Institute Finland (Luke), Jokiniemenkuja 1, POB 18, 01301 Vantaa, Finland.
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18
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Vainio EJ, Jurvansuu J, Streng J, Rajamäki ML, Hantula J, Valkonen JPT. Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs. J Gen Virol 2014; 96:714-725. [PMID: 25480928 DOI: 10.1099/jgv.0.000003] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of virus-derived small RNAs with high-throughput sequencing has been successful for detecting novel viruses in plants and invertebrates. However, the applicability of this method has not been demonstrated in fungi, although fungi were among the first organisms reported to utilize RNA silencing. Here, we used virus-infected isolates of the fungal species complex Heterobasidion annosum sensu lato as a model system to test whether mycovirus genome segments can be detected with small RNA deep sequencing. Species of the genus Heterobasidion are some of the most devastating forest pathogens in boreal forests. These fungi cause wood decay and are commonly infected with species of the family Partitiviridae and the unassigned virus species Heterobasidion RNA virus 6. Small RNA deep sequencing allowed the simultaneous detection of all eight double-stranded RNA virus strains known to be present in the tested samples and one putative mitovirus species (family Narnaviridae) with a single-stranded RNA genome, designated here as Heterobasidion mitovirus 1. Prior to this study, no members of the family Narnaviridae had been described as infecting species of Heterobasidion. Quantification of viral double- and single-stranded RNA with quantitative PCR indicated that co-infecting viral species and viruses with segmented genomes can be detected with small RNA deep sequencing despite vast differences in the amount of RNA. This is the first study demonstrating the usefulness of this method for detecting fungal viruses. Moreover, the results suggest that viral genomes are processed into small RNAs by different species of Heterobasidion.
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Affiliation(s)
- Eeva J Vainio
- Finnish Forest Research Institute, Vantaa Research Unit, Jokiniemenkuja 1, Vantaa, Finland
| | - Jaana Jurvansuu
- Finnish Forest Research Institute, Vantaa Research Unit, Jokiniemenkuja 1, Vantaa, Finland
| | - Janne Streng
- Department of Agricultural Sciences, P.O. Box 27, University of Helsinki, FI-00014 Helsinki, Finland
| | - Minna-Liisa Rajamäki
- Department of Agricultural Sciences, P.O. Box 27, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jarkko Hantula
- Finnish Forest Research Institute, Vantaa Research Unit, Jokiniemenkuja 1, Vantaa, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, P.O. Box 27, University of Helsinki, FI-00014 Helsinki, Finland
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19
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Feng Z, Zhu H, Li Z, Shi Y, Zhao L, Liu L, Jiang D. Complete genome sequence of a novel dsRNA mycovirus isolated from the phytopathogenic fungus Verticillium dahliae Kleb. Arch Virol 2013; 158:2621-3. [DOI: 10.1007/s00705-013-1774-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/21/2013] [Indexed: 11/28/2022]
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