1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Ye L, Shi X, He Y, Chen J, Xu Q, Shafik K, Fu L, Yin Y, Kotta-Loizou I, Xu W. A novel botybirnavirus with a unique satellite dsRNA causes latent infection in Didymella theifolia isolated from tea plants. Microbiol Spectr 2023; 11:e0003323. [PMID: 37962342 PMCID: PMC10714997 DOI: 10.1128/spectrum.00033-23] [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: 03/22/2023] [Accepted: 10/02/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE A novel botybirnavirus, infecting the tea plant pathogen Didymella theifolia and tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1), together with an additional double-stranded RNA (dsRNA), was characterized. DtBRV1 comprises two dsRNAs (1 and 2) encapsidated in isometric virions, while dsRNA3 is a satellite. The satellite represents a unique specimen since it contains a duplicated region and has high similarity to the two botybirnavirus dsRNAs, supporting the notion that it most likely originated from a deficient genomic component. The biological characteristics of DtBRV1 were further determined. With their unique molecular traits, DtBRV1 and its related dsRNA expand our understanding of virus diversity, taxonomy, and evolution.
Collapse
Affiliation(s)
- Liangchao Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Xinyu Shi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Yunqiang He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Jiao Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Qingeng Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Karim Shafik
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Lanning Fu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Yumeng Yin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Wenxing Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| |
Collapse
|
3
|
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.
Collapse
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.)
| | | |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Chen Z, Chen L, Anane RF, Wang Z, Gao L, Li S, Wen G, Yu D, Zhao M. Complete genome sequence of a novel mitovirus detected in Paris polyphylla var. yunnanensis. Arch Virol 2022; 167:645-650. [PMID: 35037104 DOI: 10.1007/s00705-021-05339-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
Paris mitovirus 1 (ParMV1) is a positive-sense RNA virus that was detected in diseased Paris polyphylla var. yunnanensis plants in Wenshan, Yunnan. The complete genome sequence of ParMV1 is 2,751 nucleotides in length, and the genome structure is typical of mitoviruses. The ParMV1 genome has a single open reading frame (ORF; nt 358-2,637) that encodes an RNA-dependent RNA polymerase (RdRp) with a predicted molecular mass of 86.42 kDa. ParMV1 contains six conserved motifs (Ι-VΙ) that are unique to mitoviruses. The 5' and 3' termini of the genome are predicted to have a stable secondary structure, with the reverse complementary sequence forming a panhandle structure. Comparative genome analysis revealed that the RdRp of ParMV1 shares 23.1-40.6% amino acid (aa) and 32.3-45.7% nucleotide (nt) sequence identity with those of other mitoviruses. Phylogenetic analysis based on RdRp aa sequences showed that ParMV1 clusters with mitoviruses and hence should be considered a new member of the genus Mitovirus in the family Mitoviridae. This is the first report of a novel mitovirus infecting Paris polyphylla var. yunnanensis.
Collapse
Affiliation(s)
- Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Lu Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Rex Frimpong Anane
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.,State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Zhe Wang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Like Gao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Guosong Wen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Daihong Yu
- Plant Protection and Quarantine Station of Yuanjiang County, Yuxi, 653300, Yunnan, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China. .,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China.
| |
Collapse
|
7
|
Shafik K, Umer M, You H, Aboushedida H, Wang Z, Ni D, Xu W. Characterization of a Novel Mitovirus Infecting Melanconiella theae Isolated From Tea Plants. Front Microbiol 2021; 12:757556. [PMID: 34867881 PMCID: PMC8635788 DOI: 10.3389/fmicb.2021.757556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
A dsRNA segment was identified in the fungus Melanconiella theae isolated from tea plants. The complete dsRNA sequence, determined by random cloning together with RACE protocol, is 2,461 bp in length with an AU-rich content (62.37%) and comprises a single ORF of 2,265-nucleotides encoding an RNA-dependent RNA-polymerase (RdRp, 754 amino acids in size). The terminus sequences can fold into predicted stable stem-loop structures. A BLASTX and phylogenetic analysis revealed the dsRNA genome shows similarities with the RdRp sequences of mitoviruses, with the highest identity of 48% with those of grapevine-associated mitovirus 20 and Colletotrichum fructicola mitovirus 1. Our results reveal a novel member, tentatively named Melanconiella theae mitovirus 1 (MtMV1), belongs to the family Mitoviridae. MtMV1 is capsidless as examined by transmission electron microscope, efficiently transmitted through conidia as 100 conidium-generated colonies were analyzed, and easily eliminated by hyphal tipping method combined with green-leaf tea powder. MtMV1 has a genomic sequence obviously divergent from those of most members in the family Mitoviridae and some unique characteristics unreported in known members. This is the first report of a mycovirus infecting Melanconiella fungi to date.
Collapse
Affiliation(s)
- Karim Shafik
- Hubei Hongshan Laboratory, Wuhan, China
- Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Umer
- Hubei Hongshan Laboratory, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huafeng You
- Hubei Hongshan Laboratory, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hamdy Aboushedida
- Hubei Hongshan Laboratory, Wuhan, China
- Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhenhua Wang
- Technology Center of Wuhan Customs District, Wuhan, China
| | - Dejiang Ni
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Wenxing Xu
- Hubei Hongshan Laboratory, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Wenxing Xu,
| |
Collapse
|
8
|
Molecular characterization of a new mitovirus hosted by the ectomycorrhizal fungus Albatrellopsis flettii. Arch Virol 2021; 166:3449-3454. [PMID: 34554305 DOI: 10.1007/s00705-021-05250-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
The complete genome of a novel mycovirus, Albatrellopsis flettii mitovirus 1 (AfMV1), hosted by the basidiomycetous ectomycorrhizal fungus Albatrellopsis flettii (Morse ex Pouzar) Audet, was sequenced and analyzed. The full-length cDNA sequence, obtained from a dsRNA replication intermediate of the AfMV1 genome, is 3037 bp in length with a predicted G+C content of 40.66%. Sequence analysis revealed that a single large open reading frame (ORF) is present on the positive strand when the mold mitochondrial genetic code is applied. The single ORF encodes a putative RNA-dependent RNA polymerase of 859 amino acids with a predicted molecular weight of 97.05 kDa that shares the closest similarity with the corresponding protein of Entomophthora muscae mitovirus 7, with 43.38% sequence identity. Phylogenetic analysis showed that AfMV1 could be classified as a new member of the genus Mitovirus within the family Mitoviridae. This is the first report of the complete genome sequence of a new mitovirus, AfMV1, isolated from the basidiomycetous ectomycorrhizal fungus A. flettii.
Collapse
|
9
|
Rumbou A, Vainio EJ, Büttner C. Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems. Microorganisms 2021; 9:microorganisms9081730. [PMID: 34442809 PMCID: PMC8399312 DOI: 10.3390/microorganisms9081730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.
Collapse
Affiliation(s)
- Artemis Rumbou
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
- Correspondence:
| | - Eeva J. Vainio
- Natural Resources Institute Finland, Forest Health and Biodiversity, Latokartanonkaari 9, 00790 Helsinki, Finland;
| | - Carmen Büttner
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
| |
Collapse
|
10
|
Molecular characterization of a new endornavirus inhabiting the ectomycorrhizal fungus Hygrophorus penarioides. Braz J Microbiol 2021; 52:1167-1172. [PMID: 33900612 DOI: 10.1007/s42770-021-00500-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022] Open
Abstract
Viruses hosted by uncultivated fungi have been poorly studied. We carried out studies to characterize a large dsRNA segment (~20 kbp) detected in the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides. The dsRNA was gel-purified and its randomly amplified cDNA fragments were used for high throughput sequencing (HTS). Reads were de novo assembled and BLASTx analysis revealed sequence similarity to viruses of the family Endornaviridae. The 5' and 3' terminal sequences of the dsRNA segment were determined by performing RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE). The full-length cDNA sequence of the putative endornavirus comprises 16,785 nt and contains a single, long open reading frame which encodes for a polyprotein of 5522 aa with conserved domains for cysteine-rich region, helicase, glycosyltransferase, and RNA-dependent RNA polymerase. The virus was named Hygrophorus penarioides endornavirus 1 (HpEnV1). A BLASTp search performed using the polyprotein sequence revealed that the most closely related, fully sequenced endornavirus to HpEnV1 is Ceratobasidium endornavirus B.
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Sahin E, Keskin E, Akata I. Novel and diverse mycoviruses co-inhabiting the hypogeous ectomycorrhizal fungus Picoa juniperi. Virology 2020; 552:10-19. [PMID: 33032032 DOI: 10.1016/j.virol.2020.09.009] [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: 08/16/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Viruses hosted by ectomycorrhizal fungi remain poorly studied. In this study, we detected eight new fungal viruses co-infecting a single isolate of the hypogeous ectomycorrhizal fungus Picoa juniperi using high-throughput sequencing. Phylogenetic analysis of one identified virus abbreviated as PjMTV1 revealed its closest relatives as members of the newly proposed family "Megatotiviridae". Phylogenetic analyses of two identified viruses abbreviated as PjV1 and PjV2 showed that these viruses are associated with members of the proposed family "Fusagraviridae". Phylogenetic analysis of the identified one another virus abbreviated as PjYV1 demonstrated that this virus is related to the members of the proposed family Yadokariviridae. The remaining four identified virus-like contigs were determined as segments of the bipartite dsRNA mycoviruses from the family Partitiviridae. The mycoviruses reported in this study are the first viruses described in Picoa juniperi, and PjMTV1 characterized herein is the secondly reported member of the newly proposed family "Megatotiviridae".
Collapse
Affiliation(s)
- Ergin Sahin
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey.
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Ankara University Faculty of Agriculture Department of Fisheries and Aquaculture, 06110, Dışkapı, Ankara, Turkey
| | - Ilgaz Akata
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey
| |
Collapse
|
13
|
Perlińska-Lenart U, Piłsyk S, Gryz E, Turło J, Hilszczańska D, Kruszewska JS. Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.). Arch Microbiol 2020; 202:2727-2738. [PMID: 32734321 PMCID: PMC7538415 DOI: 10.1007/s00203-020-02002-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 11/29/2022]
Abstract
Tuber species may be regarded as complex microhabitats hosting diverse microorganisms inside their fruiting bodies. Here, we investigated the structure of microbial communities inhabiting the gleba of wild growing (in stands) T. aestivum, using Illumina sequencing and culture-based methods. The two methods used in combination allowed to extract more information on complex microbiota of Tuber aestivum gleba. Analysis of the V3-V4 region of 16S rDNA identified nine phyla of bacteria present in the gleba of T. aestivum ascomata, mostly Proteobacteria from the family Bradyrhizobiaceae. Our results ideally match the earlier data for other Tuber species where the family Bradyrhizobiaceae was the most represented. The ITS1 region of fungal rDNA represented six alien fungal species belonging to three phyla. To complement the metagenomic analysis, cultivable fungi and bacteria were obtained from the gleba of the same T. aestivum fruiting bodies. The identified fungi mostly belong to the phylum Basidiomycota and same to Ascomycota. Analysis of cultivable bacteria revealed that all the specimens were colonized by different strains of Bacillus. Fungal community inhabiting T. aestivum fruiting bodies was never shown before.
Collapse
Affiliation(s)
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Gryz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jadwiga Turło
- Department of Drug Technology and Pharmaceutical Biotechnology, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Hilszczańska
- Department of Forest Ecology, Forest Research Institute, Sękocin Stary, Poland.
| | - Joanna S Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
14
|
Vainio EJ, Sutela S. Mixed infection by a partitivirus and a negative-sense RNA virus related to mymonaviruses in the polypore fungus Bondarzewia berkeleyi. Virus Res 2020; 286:198079. [PMID: 32599089 DOI: 10.1016/j.virusres.2020.198079] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/30/2022]
Abstract
Virus communities of forest fungi remain poorly characterized. In this study, we detected two new viruses co-infecting an isolate of the polypore fungus Bondarzewia berkeleyi using high-throughput sequencing. One of them was a putative new partitivirus designated as Bondarzewia berkeleyi partitivirus 1 (BbPV1), with two linear dsRNA genome segments of 1928 and 1863 bp encoding a putative RNA-dependent RNA polymerase (RdRP) of 591 aa and a putative capsid protein of 538 aa. The other virus, designated as Bondarzewia berkeleyi negative-strand RNA virus 1 (BbNSRV1), had a non-segmented negative-sense RNA genome of 10,983 nt and was related to members of family Mymonaviridae. The BbNSRV1 genome includes six predicted open reading frames (ORFs) of 279, 425, 230, 174, 200 and 1970 aa. The longest ORF contained conserved regions corresponding to Mononegavirales RdRP and mRNA-capping enzyme region V constituting the mononegavirus Large protein. In addition, a low level of sequence identity was detected between the putative nucleocapsid protein-coding ORF2 of Lentinula edodes negative-strand RNA virus 1 and BbNSRV1. The viruses characterized in this study are the first ones described in Bondarzewia spp., and BbNSRV1 is the second mymona-like virus described in a basidiomycete host.
Collapse
Affiliation(s)
- Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland.
| | - Suvi Sutela
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| |
Collapse
|
15
|
Sutela S, Vainio EJ. Virus population structure in the ectomycorrhizal fungi Lactarius rufus and L. tabidus at two forest sites in Southern Finland. Virus Res 2020; 285:197993. [PMID: 32360299 DOI: 10.1016/j.virusres.2020.197993] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/25/2020] [Accepted: 04/25/2020] [Indexed: 01/27/2023]
Abstract
Lactarius fungi belong to the Russulaceae family and have an important ecological role as ectomycorrhizal symbionts of coniferous and deciduous trees. Two Lactarius species, L. tabidus and L. rufus have been shown to harbor bisegmented dsRNA viruses belonging to an unclassified virus group including the mutualistic Curvularia thermal tolerance virus (CThTV). In this study, we characterized the first complete genome sequences of these viruses designated as Lactarius tabidus RNA virus 1 (LtRV1) and Lactarius rufus RNA virus 1 (LrRV1), both of which included two genome segments of 2241 and 2049 bp. We also analyzed spatial distribution and sequence diversity of the viruses in sixty host strains at two forest sites, and showed that the viruses are species-specific at sites where both host species co-occur. We also found that single virus isolates inhabited several different conspecific host strains, and were involved in persistent infections during up to eight years.
Collapse
Affiliation(s)
- Suvi Sutela
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland.
| | - Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland.
| |
Collapse
|
17
|
Sahin E, Akata I. Complete genome sequence of a novel mitovirus from the ectomycorrhizal fungus Geopora sumneriana. Arch Virol 2019; 164:2853-2857. [PMID: 31377887 DOI: 10.1007/s00705-019-04367-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/09/2019] [Indexed: 01/01/2023]
Abstract
A double-stranded RNA (dsRNA) segment was extracted from the ectomycorrhizal fungus Geopora sumneriana (Cooke) M. Torre, and its full-length cDNA sequence, comprising 3146 nucleotides, was determined. Sequence analysis revealed the presence of a large open reading frame (ORF) on the positive strand of this dsRNA segment when the mold mitochondrial genetic code was applied. The ORF encodes a putative RNA-dependent RNA polymerase (RdRp), which shares the highest degree of similarity with Tuber excavatum mitovirus, with 37.52% identity. This dsRNA segment represents the genome replication intermediate of a novel mitovirus that was tentatively designated as "Geopora sumneriana mitovirus 1" (GsMV1). Phylogenetic analysis further suggested that GsMV1 is a member of the family Narnaviridae. This is the first study reporting on a mitovirus genome sequence in the ectomycorrhizal fungus G. sumneriana.
Collapse
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
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Khankhum S, Sela N, Osorno JM, Valverde RA. RNAseq Analysis of Endornavirus-Infected vs. Endornavirus-Free Common Bean ( Phaseolus vulgaris) Cultivar Black Turtle Soup. Front Microbiol 2016; 7:1905. [PMID: 27965640 PMCID: PMC5126043 DOI: 10.3389/fmicb.2016.01905] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 12/30/2022] Open
Affiliation(s)
- Surasak Khankhum
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center Baton Rouge, LA, USA
| | - Noa Sela
- Department of Plant Pathology and Weed Research, The Volcani Center-ARO Bet-Dagan, Israel
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University Fargo, ND, USA
| | - Rodrigo A Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center Baton Rouge, LA, USA
| |
Collapse
|
22
|
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.
Collapse
|
23
|
Petrzik K, Sarkisova T, Starý J, Koloniuk I, Hrabáková L, Kubešová O. Molecular characterization of a new monopartite dsRNA mycovirus from mycorrhizal Thelephora terrestris (Ehrh.) and its detection in soil oribatid mites (Acari: Oribatida). Virology 2016; 489:12-9. [DOI: 10.1016/j.virol.2015.11.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/04/2015] [Accepted: 11/10/2015] [Indexed: 02/06/2023]
|
24
|
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]
|
25
|
The Role of the Microbiome of Truffles in Aroma Formation: a Meta-Analysis Approach. Appl Environ Microbiol 2015; 81:6946-52. [PMID: 26187969 DOI: 10.1128/aem.01098-15] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Truffles (Tuber spp.) are ascomycete subterraneous fungi that form ectomycorrhizas in a symbiotic relationship with plant roots. Their fruiting bodies are appreciated for their distinctive aroma, which might be partially derived from microbes. Indeed, truffle fruiting bodies are colonized by a diverse microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses. The aim of this minireview is two-fold. First, the current knowledge on the microbial community composition of truffles has been synthesized to highlight similarities and differences among four truffle (Tuber) species (T. magnatum, T. melanosporum, T. aestivum, and T. borchii) at various stages of their life cycle. Second, the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one hand, odorants, which are common to many truffle species, might be of mixed truffle and microbial origin, while on the other hand, less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the microbiome of the truffle, might also be the most important contributors to truffle aroma not only in T. borchii, as already demonstrated, but also in T. magnatum, T. aestivum, and T. melanosporum.
Collapse
|
26
|
Detection and genetic characterisation of a novel mycovirus in Hymenoscyphus fraxineus, the causal agent of ash dieback. INFECTION GENETICS AND EVOLUTION 2014; 28:78-86. [DOI: 10.1016/j.meegid.2014.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 12/11/2022]
|
27
|
Jiang D, Fu Y, Guoqing L, Ghabrial SA. Viruses of the plant pathogenic fungus Sclerotinia sclerotiorum. Adv Virus Res 2013; 86:215-48. [PMID: 23498908 DOI: 10.1016/b978-0-12-394315-6.00008-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Sclerotinia sclerotiorum is a notorious plant fungal pathogen with a broad host range including many important crops, such as oilseed rape, soybean, and numerous vegetable crops. Hypovirulence-associated mycoviruses have attracted much attention because of their potential as biological control agents for combating plant fungal diseases and for use in fundamental studies on fungal pathogenicity and other properties. This chapter describes several mycoviruses that were isolated from hypovirulent strains except for strain Sunf-M, which has a normal phenotype. These viruses include the geminivirus-like mycovirus Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), Sclerotinia debilitation-associated RNA virus (SsDRV), Sclerotinia sclerotiorum RNA virus L (SsRV-L), Sclerotinia sclerotiorum hypovirus 1 (SsHV-1), Sclerotinia sclerotiorum mitoviruses 1 and 2 (SsMV-1, SsMV-2), and Sclerotinia sclerotiorum partitivirus S (SsPV-S). Unlike many other fungi, incidences of mixed infections with two or more mycoviruses in S. sclerotiorum are particularly high and very common. The interaction between SsDRV and S. sclerotiorum is likely to be unique. The significance of these mycoviruses to fungal ecology and viral evolution and the potential for biological control of Sclerotinia diseases using mycoviruses are discussed.
Collapse
Affiliation(s)
- Daohong Jiang
- The State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | | | | | | |
Collapse
|
28
|
Abstract
Members of the virus family Narnaviridae contain the simplest genomes of any RNA virus, ranging from 2.3 to 3.6 kb and encoding only a single polypeptide that has an RNA-dependent RNA polymerase domain. The family is subdivided into two genera based on subcellular location: members of the genus Narnavirus have been found in the yeast Saccharomyces cerevisiae and in the oomycete Phytophthora infestans and are confined to the cytosol, while members of the genus Mitovirus have been found only in filamentous fungi and are found in mitochondria. None identified thus far encodes a capsid protein; like several other RNA viruses of lower eukaryotes, their genomes are confined within lipid vesicles. As more family members are discovered, their importance as genetic elements is becoming evident. The unique association of the genus Mitovirus with mitochondria renders them potentially valuable tools to study biology of lower eukaryotes.
Collapse
|
29
|
Xie J, Ghabrial SA. Molecular characterization of two mitoviruses co-infecting a hypovirulent isolate of the plant pathogenic fungus Sclerotinia sclerotiorum [corrected]. Virology 2012; 428:77-85. [PMID: 22520836 DOI: 10.1016/j.virol.2012.03.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/26/2012] [Accepted: 03/17/2012] [Indexed: 11/30/2022]
Abstract
The complete nucleotide sequences of two double-stranded RNA (dsRNA) segments, isolated from the same hypovirulent strain (KL-1) of Sclerotinia sclerotiorum, were determined. Sequence analysis showed that dsRNAs 1 to be 2513 nts long and is A-U rich (61.7%). Excluding the poly(A) tail, dsRNAs2 is 2421 nts long and its AU content is 53.1%. The 5' and 3'-terminal sequences of the positive-strand of each dsRNA could be folded into predicted stable stem-loop structures. Mitochondrial codon usage revealed that each dsRNA has a single large open reading frame coding for a protein containing RNA-dependent RNA polymerase conserved motifs. Furthermore, dsRNAs 1 and 2 share sequence similarities with other mitoviruses. These results suggest that dsRNAs 1 and 2 represent two distinct new mitoviruses, designated Sclerotinia sclerotiorum mitovirus 1 (SsMV1/KL-1) and SsMV2/KL-1, respectively. The hypovirulence traits of strain KL-1 and the two mitoviruses could be co-transmitted to a virus-free virulent strain via hyphal anastomosis.
Collapse
Affiliation(s)
- Jiatao Xie
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA
| | | |
Collapse
|
30
|
Ikeda Y, Shimura H, Kitahara R, Masuta C, Ezawa T. A novel virus-like double-stranded RNA in an obligate biotroph arbuscular mycorrhizal fungus: a hidden player in mycorrhizal symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1005-1012. [PMID: 22414436 DOI: 10.1094/mpmi-11-11-0288] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi form mutualistic associations with most land plants and enhance phosphorus uptake of the host plants. Fungal viruses (mycoviruses) that possess a double-stranded RNA (dsRNA) genome often affect plant-fungal interactions via altering phenotypic expression of their host fungi. The present study demonstrates, for the first time, the presence of dsRNAs, which are highly likely to be mycoviruses, in AM fungi. dsRNA was extracted from mycelia of Glomus sp. strain RF1, purified, and subjected to electrophoresis. The fungus was found to harbor various dsRNA segments that differed in size. Among them, a 4.5-kbp segment was termed Glomus sp. strain RF1 virus-like medium dsRNA (GRF1V-M) and characterized in detail. The GRF1V-M genome segment was 4,557 nucleotides in length and encoded RNA-dependent RNA polymerase and a structural protein. GRF1V-M was phylogenetically distinct and could not be assigned to known genera of mycovirus. The GRF1V-M-free culture line of Glomus sp. strain RF1, which was raised by single-spore isolation, produced twofold greater number of spores and promoted plant growth more efficiently than the GRF1V-M-positive lines. These observations suggest that mycoviruses in AM fungi, at least some of them, have evolved under unique selection pressures and are a biologically active component in the symbiosis.
Collapse
Affiliation(s)
- Yoji Ikeda
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | | | | | | | | |
Collapse
|
31
|
Heinze C. A novel mycovirus from Clitocybe odora. Arch Virol 2012; 157:1831-4. [PMID: 22678719 DOI: 10.1007/s00705-012-1373-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 05/06/2012] [Indexed: 11/30/2022]
Abstract
The Ninth Report of the International Committee on Taxonomy of Viruses (ICTV) reports only a few species whose members replicate in fungi. Most of these mycoviruses are described to replicate in phytopathogenic and commercially cultivated fungi. A few reports describe virus-like symptoms and virus-like particles in non-cultivated basidiocarps such as Boletus edulis, Laccaria spp. and Cantharellus spp. However, viral sequences from non-cultivated Agaricomycotina are not available yet. In this report, I present a partial sequence of a virus found in Clitocybe odora (Bull.:Fr.) P. Kumm var. odora coding for a putative RNA-dependent RNA polymerase (RdRp) and a small 20-kDa ORF that may encode a coat protein (CP). The sequence of the putative RdRp (ORF 1) of C. odora clusters with those of the Tanathephorus cucumeris virus RdRp and the Tuber aestivum mitovirus RdRp. In addition to sequence homology, Tanathephorus cucumeris virus shows a similar codon usage and TA content in the 5'- and 3' non-translated regions, but it does not encode a putative CP. A viral DNA form proposed for Tanathephorus cucumeris virus was not found in Clitocybe odora. This viral sequence does not fit into any of the existing virus taxa.
Collapse
Affiliation(s)
- Cornelia Heinze
- University of Hamburg, Biocenter Klein Flottbek, Ohnhorststr. 18, 22609 Hamburg, Germany.
| |
Collapse
|
32
|
Stielow JB, Bratek Z, Klenk HP, Winter S, Menzel W. A novel mitovirus from the hypogeous ectomycorrhizal fungus Tuber excavatum. Arch Virol 2012; 157:787-790. [DOI: 10.1007/s00705-012-1228-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 12/07/2011] [Indexed: 11/30/2022]
|
33
|
Göker M, Scheuner C, Klenk HP, Stielow JB, Menzel W. Codivergence of mycoviruses with their hosts. PLoS One 2011; 6:e22252. [PMID: 21829452 PMCID: PMC3146478 DOI: 10.1371/journal.pone.0022252] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/17/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The associations between pathogens and their hosts are complex and can result from any combination of evolutionary events such as codivergence, switching, and duplication of the pathogen. Mycoviruses are RNA viruses which infect fungi and for which natural vectors are so far unknown. Thus, lateral transfer might be improbable and codivergence their dominant mode of evolution. Accordingly, mycoviruses are a suitable target for statistical tests of virus-host codivergence, but inference of mycovirus phylogenies might be difficult because of low sequence similarity even within families. METHODOLOGY We analyzed here the evolutionary dynamics of all mycovirus families by comparing virus and host phylogenies. Additionally, we assessed the sensitivity of the co-phylogenetic tests to the settings for inferring virus trees from their genome sequences and approximate, taxonomy-based host trees. CONCLUSIONS While sequence alignment filtering modes affected branch support, the overall results of the co-phylogenetic tests were significantly influenced only by the number of viruses sampled per family. The trees of the two largest families, Partitiviridae and Totiviridae, were significantly more similar to those of their hosts than expected by chance, and most individual host-virus links had a significant positive impact on the global fit, indicating that codivergence is the dominant mode of virus diversification. However, in this regard mycoviruses did not differ from closely related viruses sampled from non-fungus hosts. The remaining virus families were either dominated by other evolutionary modes or lacked an apparent overall pattern. As this negative result might be caused by insufficient taxon sampling, the most parsimonious hypothesis still is that host-parasite evolution is basically the same in all mycovirus families. This is the first study of mycovirus-host codivergence, and the results shed light not only on how mycovirus biology affects their co-phylogenetic relationships, but also on their presumable host range itself.
Collapse
Affiliation(s)
- Markus Göker
- DSMZ-German Collection for Microorganisms and Cell Cultures, Braunschweig, Germany.
| | | | | | | | | |
Collapse
|