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Fan Y, Zhao W, Tang X, Yang M, Yang Y, Zhang Z, Cheng B, Zhou E, He Z. Co-infection of Four Novel Mycoviruses from Three Lineages Confers Hypovirulence on Phytopathogenic Fungus Ustilaginoidea virens. RICE (NEW YORK, N.Y.) 2024; 17:44. [PMID: 39014281 PMCID: PMC11252108 DOI: 10.1186/s12284-024-00721-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/21/2024] [Indexed: 07/18/2024]
Abstract
Rice false smut caused by Ustilaginoidea virens has become one of the most important diseases of rice. Mycoviruses are viruses that can infect fungi with the potential to control fungal diseases. However, little is known about the biocontrol role of hypoviruses in U. virens. In this study, we revealed that the hypovirulence-associated U. virens strain Uv325 was co-infected by four novel mycoviruses from three lineages, designated Ustilaginoidea virens RNA virus 16 (UvRV16), Ustilaginoidea virens botourmiavirus virus 8 (UvBV8), Ustilaginoidea virens botourmiavirus virus 9 (UvBV9), and Ustilaginoidea virens narnavirus virus 13 (UvNV13), respectively. The U. virens strain co-infected by four mycoviruses showed slower growth rates, reduced conidial yield, and attenuated pigmentation. We demonstrated that UvRV16 was not only the major factor responsible for the hypovirulent phenotype in U. vriens, but also able to prevent U. virens to accumulate more mycotoxin, thereby weakening the inhibitory effects on rice seed germination and seedling growth. Additionally, we indicated that UvRV16 can disrupt the antiviral response of U. virens by suppressing the transcriptional expression of multiple genes involved in autophagy and RNA silencing. In conclusion, our study provided new insights into the biological control of rice false smut.
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Affiliation(s)
- Yu Fan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenhua Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaolin Tang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Mei Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yingqing Yang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Zixuan Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Baoping Cheng
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Key Laboratory of Green Prevention and Control On Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong, 510642, China.
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhenrui He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
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2
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Ding H, Wang Y, Li C, Shuai S, An H, Fang S, Zhang S, Deng Q. Molecular characterization of a single-negative-stranded RNA virus from the rice blast fungus Magnaporthe oryzae isolate NJ39. Arch Virol 2024; 169:128. [PMID: 38802709 DOI: 10.1007/s00705-024-06054-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/29/2024] [Indexed: 05/29/2024]
Abstract
A novel negative-sense single-stranded RNA mycovirus, designated as "Magnaporthe oryzae mymonavirus 1" (MoMNV1), was identified in the rice blast fungus Magnaporthe oryzae isolate NJ39. MoMNV1 has a single genomic RNA segment consisting of 10,515 nucleotides, which contains six open reading frames. The largest open reading frame contains 5837 bases and encodes an RNA replicase. The six open reading frames have no overlap and are arranged linearly on the genome, but the spacing of the genes is small, with a maximum of 315 bases and a minimum of 80 bases. Genome comparison and phylogenetic analysis indicated that MoMNV1 is a new member of the genus Penicillimonavirus of the family Mymonaviridae.
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Affiliation(s)
- Hang Ding
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Yao Wang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Cong Li
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Simin Shuai
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Hongliu An
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China
| | - Shouguo Fang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China
| | - Songbai Zhang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China
| | - Qingchao Deng
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China.
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China.
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3
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Song X, Zhang J, Ma Q, Wang Y, Guo Y, Guo L, Wu H, Zhang M. Molecular characterization of a novel narnavirus infecting the phytopathogenic fungus Botryosphaeria dothidea. Arch Virol 2024; 169:38. [PMID: 38300296 DOI: 10.1007/s00705-024-05964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/03/2023] [Indexed: 02/02/2024]
Abstract
Here, a novel mycovirus, Botryosphaeria dothidea narnavirus 5 (BdNV5), was discovered in the plant-pathogenic fungus Botryosphaeria dothidea strain ZM210167-1. The BdNV5 genome sequence is 2,397 nucleotides (nt) in length and contains a putative open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp) with a molecular mass of 72.77 kDa. A BLASTp search using the RdRp amino acid (aa) sequence showed that it was most similar to the RdRp of Botryosphaeria dothidea narnavirus 4 (42.35%). In a phylogenetic tree based on RdRp aa sequences, BdNV5 clustered with members of the family Narnaviridae. BdNV5 is thus a novel member of the family Narnaviridae infecting the phytopathogenic fungus B. dothidea.
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Affiliation(s)
- Xinzheng Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Jianing Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Qingzhou Ma
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Yanfen Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Yashuang Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China
| | - Haiyan Wu
- Analytical Instrument Center, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
| | - Meng Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, 100193, China.
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4
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de Santana SF, Santos VC, Lopes ÍS, Porto JAM, Mora-Ocampo IY, Sodré GA, Pirovani CP, Góes-Neto A, Pacheco LGC, Fonseca PLC, Costa MA, Aguiar ERGR. Mining Public Data to Investigate the Virome of Neglected Pollinators and Other Floral Visitors. Viruses 2023; 15:1850. [PMID: 37766257 PMCID: PMC10535300 DOI: 10.3390/v15091850] [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: 03/14/2023] [Revised: 07/31/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
This study reports the virome investigation of pollinator species and other floral visitors associated with plants from the south of Bahia: Aphis aurantii, Atrichopogon sp., Dasyhelea sp., Forcipomyia taiwana, and Trigona ventralis hoozana. Studying viruses in insects associated with economically important crops is vital to understand transmission dynamics and manage viral diseases that pose as threats for global food security. Using literature mining and public RNA next-generation sequencing data deposited in the NCBI SRA database, we identified potential vectors associated with Malvaceae plant species and characterized the microbial communities resident in these insects. Bacteria and Eukarya dominated the metagenomic analyses of all taxon groups. We also found sequences showing similarity to elements from several viral families, including Bunyavirales, Chuviridae, Iflaviridae, Narnaviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, and Xinmoviridae. Phylogenetic analyses indicated the existence of at least 16 new viruses distributed among A. aurantii (3), Atrichopogon sp. (4), Dasyhelea sp. (3), and F. taiwana (6). No novel viruses were found for T. ventralis hoozana. For F. taiwana, the available libraries also allowed us to suggest possible vertical transmission, while for A. aurantii we followed the infection profile along the insect development. Our results highlight the importance of studying the virome of insect species associated with crop pollination, as they may play a crucial role in the transmission of viruses to economically important plants, such as those of the genus Theobroma, or they will reduce the pollination process. This information may be valuable in developing strategies to mitigate the spread of viruses and protect the global industry.
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Affiliation(s)
- Sabrina Ferreira de Santana
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
| | - Vinícius Castro Santos
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil (A.G.-N.)
| | - Ícaro Santos Lopes
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil (A.G.-N.)
| | - Joel Augusto Moura Porto
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
| | - Irma Yuliana Mora-Ocampo
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
| | - George Andrade Sodré
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
| | - Carlos Priminho Pirovani
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
| | - Aristóteles Góes-Neto
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil (A.G.-N.)
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Luis Gustavo Carvalho Pacheco
- Department of Biotechnology, Institute of Health Sciences, Universidade Federal da Bahia, Salvador 40231-300, BA, Brazil
| | - Paula Luize Camargos Fonseca
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
- Department of Genetics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Marco Antônio Costa
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (S.F.d.S.)
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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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6
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Zhao C, Li S, Ma Z, Wang W, Gao L, Han C, Yang A, Wu X. Anastomosis Groups and Mycovirome of Rhizoctonia Isolates Causing Sugar Beet Root and Crown Rot and Their Sensitivity to Flutolanil, Thifluzamide, and Pencycuron. J Fungi (Basel) 2023; 9:jof9050545. [PMID: 37233256 DOI: 10.3390/jof9050545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Anastomosis groups (AGs) or subgroups of 244 Rhizoctonia isolates recovered from sugar beet roots with symptoms of root and crown rot were characterized to be AG-A, AG-K, AG-2-2IIIB, AG-2-2IV, AG-3 PT, AG-4HGI, AG-4HGII, and AG-4HGIII, with AG-4HGI (108 isolates, 44.26%) and AG-2-2IIIB (107 isolates, 43.85%) being predominate. Four unclassified mycoviruses and one hundred and one putative mycoviruses belonging to six families, namely Mitoviridae (60.00%), Narnaviridae (18.10%), Partitiviridae (7.62%), Benyviridae (4.76%), Hypoviridae (3.81%), and Botourmiaviridae (1.90%), were found to be present in these 244 Rhizoctonia isolates, most of which (88.57%) contained positive single-stranded RNA genome. The 244 Rhizoctonia isolates were all sensitive to flutolanil and thifluzamide, with average median effective concentration (EC50) value of 0.3199 ± 0.0149 μg·mL-1 and 0.1081 ± 0.0044 μg·mL-1, respectively. Among the 244 isolates, except for 20 Rhizoctonia isolates (seven isolates of AG-A and AG-K, one isolate of AG-4HGI, and 12 isolates of AG-4HGII), 117 isolates of AG-2-2IIIB, AG-2-2IV, AG-3 PT, and AG-4HGIII, 107 isolates of AG-4HGI, and six isolates of AG-4HGII were sensitive to pencycuron, with average EC50 value of 0.0339 ± 0.0012 μg·mL-1. Correlation index (ρ) of cross-resistance level between flutolanil and thifluzamide, flutolanil and pencycuron, and thifluzamide and pencycuron was 0.398, 0.315, and 0.125, respectively. This is the first detailed study on AG identification, mycovirome analysis, and sensitivity to flutolanil, thifluzamide, and pencycuron of Rhizoctonia isolates associated with sugar beet root and crown rot.
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Affiliation(s)
- Can Zhao
- College of Plant Protection, China Agricultural University, Beijing 100193, China
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Siwei Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhihao Ma
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wenjun Wang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Lihong Gao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Anpei Yang
- Institute of Plant Protection, Xinjiang Academy of Agricultural Science, Urumqi 830091, China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
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7
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Zhou S, Chen D, Fu Y, Zhou J, Yang Y, Xie C, Zheng L. Characterization of a novel mycotombus-like virus from the plant-pathogenic fungus Phoma matteucciicola. Arch Virol 2023; 168:103. [PMID: 36892708 DOI: 10.1007/s00705-023-05714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/13/2023] [Indexed: 03/10/2023]
Abstract
Here, we report a novel mycotombus-like mycovirus, tentatively named "Phoma matteucciicola RNA virus 2" (PmRV2), derived from the phytopathogenic fungus Phoma matteucciicola strain HNQH1. The complete PmRV2 genome is comprised of a positive-sense single-stranded RNA (+ssRNA) of 3,460 nucleotides (nt) with a GC content of 56.71%. Sequence analysis of PmRV2 indicated the presence of two noncontiguous open reading frames (ORFs) encoding a hypothetical protein and an RNA-dependent RNA polymerase (RdRp), respectively. PmRV2 contains a metal-binding 'GDN' triplet in motif C of RdRp, while most +ssRNA mycoviruses contained a 'GDD' motif in the same region. A BLASTp search showed that the RdRp amino acid sequence of PmRV2 was most closely related to the RdRp of Macrophomina phaseolina umbra-like virus 1 (50.72% identity) and Erysiphe necator umbra-like virus 2 (EnUlV2, 44.84% identity). Phylogenetic analysis indicated that PmRV2 grouped together with EnUlV2 within the recently proposed family "Mycotombusviridae".
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Affiliation(s)
- Siyu Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, 570228, Hainan, China
| | - Daipeng Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, 570228, Hainan, China
| | - Yujia Fu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, 570228, Hainan, China
| | - Jingyi Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, 570228, Hainan, China
| | - Yingqing Yang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, 570228, Hainan, China.,Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Changping Xie
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, 570228, Hainan, China
| | - Li Zheng
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China. .,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, 570228, Hainan, China.
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8
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Reyes BMD, Fonseca PLC, Heming NM, Conceição LBDA, Nascimento KTDS, Gramacho KP, Arevalo-Gardini E, Pirovani CP, Aguiar ERGR. Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species. Front Microbiol 2023; 13:1053562. [PMID: 36817107 PMCID: PMC9936985 DOI: 10.3389/fmicb.2022.1053562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/23/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Theobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized. Methods Herein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri. Results Our data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements. Discussion To the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.
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Affiliation(s)
| | - Paula Luize Camargos Fonseca
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil,Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Neander Marcel Heming
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | | | - Karina Peres Gramacho
- Centro de Pesquisas do Cacau, Comissão Executivo do Plano da Lavoura Cacaueira, CEPEC/CEPLAC, Rodovia Ilhéus-Itabuna, Ilhéus, Brazil
| | - Enrique Arevalo-Gardini
- Instituto de Cultivos Tropicales, Tarapoto, Peru,Universidad Nacional Autónoma de Alto Amazonas, Yurimaguas, Peru
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil,*Correspondence: Eric Roberto Guimarães Rocha Aguiar, ✉
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9
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Vijayraghavan S, Kozmin SG, Xi W, McCusker JH. A novel narnavirus is widespread in Saccharomyces cerevisiae and impacts multiple host phenotypes. G3 (BETHESDA, MD.) 2022; 13:6957440. [PMID: 36560866 PMCID: PMC9911063 DOI: 10.1093/g3journal/jkac337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
RNA viruses are a widespread, biologically diverse group that includes the narnaviridiae, a family of unencapsidated RNA viruses containing a single ORF that encodes an RNA-dependent RNA polymerase. In the yeast Saccharomyces cerevisiae, the 20S and 23S RNA viruses are well-studied members of the narnaviridiae, which are present at low intracellular copy numbers, unless induced by stress or unfavorable growth conditions, and are not known to affect host fitness. In this study, we describe a new S. cerevisiae narnavirus that we designate as N1199. We show that N1199 is uniquely present as a double-stranded RNA at a high level relative to other known members of this family in 1 strain background, YJM1199, and is present as a single-stranded RNA at lower levels in 98 of the remaining 100-genomes strains. Furthermore, we see a strong association between the presence of high level N1199 and host phenotype defects, including greatly reduced sporulation efficiency and growth on multiple carbon sources. Finally, we describe associations between N1199 abundance and host phenotype defects, including autophagy.
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Affiliation(s)
- Sriram Vijayraghavan
- Present address: Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Stanislav G Kozmin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 561 Research Drive 3020, Jones Bldg. Room 239, Durham, NC 27710, USA
| | - Wen Xi
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 561 Research Drive 3020, Jones Bldg. Room 239, Durham, NC 27710, USA
| | - John H McCusker
- Corresponding author: Department of Molecular Genetics and Microbiology, Duke University Medical Center, 561 Research Drive 3020, Jones Bldg. Room 239, Durham, NC 27710, USA.
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10
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Xie FL, Zhou XY, Xiao R, Zhang CJ, Zhong J, Zhou Q, Liu F, Zhu HJ. Discovery and exploration of widespread infection of mycoviruses in Phomopsis vexans, the causal agent of phomopsis blight of eggplant in China. FRONTIERS IN PLANT SCIENCE 2022; 13:996862. [PMID: 36438156 PMCID: PMC9685175 DOI: 10.3389/fpls.2022.996862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/11/2022] [Indexed: 06/01/2023]
Abstract
Phomopsis vexans, which causes Phomopsis blight of eggplant, has been reported worldwide. To study the biocontrol of this disease, 162 leaf and fruit samples of eggplant Phomopsis blight were collected from Hunan, Hubei, Jiangxi, Sichuan, Zhejiang, Fujian, Guangdong and Anhui Provinces from 2017 to 2019. Eighty-seven pathogenic fungus isolates were identified as P. vexans. The following studies were conducted: screening of sporulation medium, spore morphology analysis, mycovirus detection and identification of novel mycoviruses in these isolates. The results showed that eggplant tissue medium was the most suitable medium for rapid sporulation, and all isolates had mycoviruses consisting of mainly mixed infections. The genome of these mycoviruses varied from 1-15 kb. Five novel mycoviruses infecting P. vexans were obtained, including "Phomopsis vexans fusarivirus 1" (PvFV1), "Phomopsis vexans ourmia-like virus 1" (PvOLV1), "Phomopsis vexans endornavirus 2" (PvEV2), "Phomopsis vexans partitivirus 1" (PvPV1) and "Phomopsis vexans victorivirus L1" (PvVVL1). Thus, PvVVL1 displays a unique genome structure, and this is the first report of a victorivirus consisting of two segments and of a deltapartitivirus infecting the fungus host.
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Affiliation(s)
- Fang Ling Xie
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xin Yu Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Rong Xiao
- Hunan Institute of Microbiology, Changsha, China
| | - Chao Jun Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Jie Zhong
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Qian Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Feng Liu
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Hong Jian Zhu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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Hai D, Li J, Lan S, Wu T, Li Y, Cheng J, Fu Y, Lin Y, Jiang D, Wang M, Xie J. Discovery and Evolution of Six Positive-Sense RNA Viruses Co-infecting the Hypovirulent Strain SCH733 of Sclerotinia sclerotiorum. PHYTOPATHOLOGY 2022; 112:2449-2461. [PMID: 35793152 DOI: 10.1094/phyto-05-22-0148-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sclerotinia sclerotiorum is a well-known phytopathogenic fungus with a wide host range. Identifying novel mycoviruses in phytopathogenic fungi is necessary to develop novel strategies for plant health protection and contribute to understanding the origin of viruses. Six new mycoviruses with positive single-stranded RNA genomes co-infecting the hypovirulent strain SCH733 of S. sclerotiorum were identified using a metatranscriptomic approach, and their complete genome sequences were molecularly determined. These mycoviruses belong to the following five families: Narnaviridae, Mitoviridae, Deltaflexviridae, Botourmiaviridae, and Ambiguiviridae. Three of these mycoviruses belong to existing International Committee on Taxonomy of Viruses (ICTV)-recognized species. Two of these newly identified mycoviruses have unique genomic features that are significantly different from those of all known mycoviruses. Phylogenetic analysis revealed that these six mycoviruses included close as well as distant relatives of known mycoviruses, thereby providing new insight into virus evolution and classification. Mycovirus horizontal transmission and elimination experiments revealed that Sclerotinia sclerotiorum narnavirus 5 is associated with hypovirulence of S. sclerotiorum, although we have not shown that it is independently responsible for the hypovirulence phenotype. This study broadens the diversity of known mycoviruses infecting S. sclerotiorum and provides a clue toward limiting hypovirulence in S. sclerotiorum.
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Affiliation(s)
- Du Hai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jincang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shangsong Lan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Tun Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ying Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Minghong Wang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, College of Forestry and Horticulture, Hubei Minzu University, Enshi, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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12
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Shuai S, Zheng H, Ding H, Wang Y, Li J, Liu F, Liu F, An H, Fang S, Zhang S, Deng Q. Molecular characterization of a novel botourmiavirus with inverted complementary termini from the rice blast fungus Magnaporthe oryzae isolate HF04. Arch Virol 2022; 167:1899-1903. [PMID: 35716263 DOI: 10.1007/s00705-022-05506-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
Abstract
A novel positive-sense single-stranded RNA mycovirus, designated as "Magnaporthe oryzae botourmiavirus 10" (MoBV10), was identified in the rice blast fungus Magnaporthe oryzae isolate HF04. MoBV10 has a single genomic RNA segment consisting of 2,448 nucleotides, which contains a single open reading frame encoding an RNA-dependent RNA polymerase. Genome comparison and phylogenetic analysis indicated that MoBV10 is a new member of the genus Betascleroulivirus in the family Botourmiaviridae. The 5'- and 3'-terminal sequences of the genomic RNA of MoBV10 have inverted complementarity and potentially form a panhandle structure, which is very rare in RNA viruses.
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Affiliation(s)
- Simnin Shuai
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Hong Zheng
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Hang Ding
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Yao Wang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Jinzhe Li
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Fuyu Liu
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Fengying Liu
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Hongliu An
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Shouguo Fang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Songbai Zhang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Qingchao Deng
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China. .,Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China.
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Abstract
Botrytis cinerea is one of the most important plant-pathogenic fungus. Products based on microorganisms can be used in biocontrol strategies alternative to chemical control, and mycoviruses have been explored as putative biological agents in such approaches. Here, we have explored the mycovirome of B. cinerea isolates from grapevine of Italy and Spain to increase the knowledge about mycoviral diversity and evolution, and to search for new widely distributed mycoviruses that could be active ingredients in biological products to control this hazardous fungus. A total of 248 B. cinerea field isolates were used for our metatranscriptomic study. Ninety-two mycoviruses were identified: 62 new mycoviral species constituting putative novel viral genera and families. Of these mycoviruses, 57 had a positive-sense single-stranded RNA (ssRNA) genome, 19 contained a double-stranded RNA (dsRNA) genome, 15 had a negative-sense ssRNA genome, and 1 contained a single-stranded DNA (ssDNA) genome. In general, ssRNA mycoviruses were widely distributed in all sampled regions, the ssDNA mycovirus was more frequently found in Spain, and dsRNA mycoviruses were scattered in some pools of both countries. Some of the identified mycoviruses belong to clades that have never been found associated with Botrytis species: Botrytis-infecting narnaviruses; alpha-like, umbra-like, and tymo-like ssRNA+ mycoviruses; trisegmented ssRNA- mycovirus; bisegmented and tetrasegmented dsRNA mycoviruses; and finally, an ssDNA mycovirus. Among the results obtained in this massive mycovirus screening, the discovery of novel bisegmented viruses, phylogenetically related to narnaviruses, is remarkable.IMPORTANCE The results obtained here have expanded our knowledge of mycoviral diversity, horizontal transfers, and putative cross-kingdom events. To date, this study presents the most extensive and wide diversity collection of mycoviruses infecting the necrotrophic fungus B. cinerea The collection included all types of mycoviruses, with dsRNA, ssRNA+, ssRNA-, and ssDNA genomes, most of which were discovered here, and some of which were previously reported as infecting B. cinerea or other plant-pathogenic fungi. Some of these mycoviruses are reported for the first time here associated with B. cinerea, as a trisegmented ssRNA- mycovirus and as an ssDNA mycovirus, but even more remarkablly, we also describe here four novel bisegmented viruses (binarnaviruses) not previously described in nature. The present findings significantly contribute to general knowledge in virology and more particularly in the field of mycovirology.
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Complete nucleotide sequence of a novel botourmiavirus from the rice blast fungus Magnaporthe oryzae isolate SH05. Arch Virol 2021; 166:1783-1787. [PMID: 33779811 DOI: 10.1007/s00705-021-05044-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/04/2021] [Indexed: 10/21/2022]
Abstract
A novel mycovirus with the proposed name "Magnaporthe oryzae botourmiavirus 9" (MoBV9) was found in the rice blast fungus Magnaporthe oryzae isolate SH05. The virus has a positive single-stranded RNA genome of 2,812 nucleotides and contains a single open reading frame predicted to encode an RNA-dependent RNA polymerase that is closely related to those of some unclassified viruses of the family Botourmiaviridae, including Plasmopara viticola lesion associated ourmia-like virus 44, Plasmopara viticola lesion associated ourmia-like virus 47, and Cladosporium uredinicola ourmiavirus 1. Genome sequence comparisons and phylogenetic analysis supported the notion that MoBV9 is a new member of the family Botourmiaviridae.
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Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum. Viruses 2021; 13:v13030375. [PMID: 33673510 PMCID: PMC7997348 DOI: 10.3390/v13030375] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/02/2023] Open
Abstract
Neofusicoccum parvum is a fungal plant-pathogen belonging to the family Botryosphaeriaceae, and is considered one of the most aggressive causal agents of the grapevine trunk disease (GTD) Botryosphaeria dieback. In this study, the mycovirome of a single strain of N. parvum (COLB) was characterized by high throughput sequencing analysis of total RNA and subsequent bioinformatic analyses. Contig annotations, genome completions, and phylogenetic analyses allowed us to describe six novel mycoviruses belonging to four different viral families. The virome is composed of two victoriviruses in the family Totiviridae, one alphaendornavirus in the family Endornaviridae, two mitoviruses in the family Mitoviridae, and one narnavirus belonging to the family Narnaviridae. The presence of the co-infecting viruses was confirmed by sequencing the RT-PCR products generated from total nucleic acids extracted from COLB. This study shows that the mycovirome of a single N. parvum strain is highly diverse and distinct from that previously described in N. parvum strains isolated from grapevines.
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Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus-Host Interaction Signatures. Viruses 2020; 13:v13010009. [PMID: 33374584 PMCID: PMC7822452 DOI: 10.3390/v13010009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of viruses is poorly understood. In this work, Lu. longipalpis RNA libraries were subjected to progressive assembly using viral profile HMMs as seeds. A sequence phylogenetically related to fungal viruses of the genus Mitovirus was identified and this novel virus was named Lul-MV-1. The 2697-base genome presents a single gene coding for an RNA-directed RNA polymerase with an organellar genetic code. To determine the possible host of Lul-MV-1, we analyzed the molecular characteristics of the viral genome. Dinucleotide composition and codon usage showed profiles similar to mitochondrial DNA of invertebrate hosts. Also, the virus-derived small RNA profile was consistent with the activation of the siRNA pathway, with size distribution and 5′ base enrichment analogous to those observed in viruses of sand flies, reinforcing Lu. longipalpis as a putative host. Finally, RT-PCR of different insect pools and sequences of public Lu. longipalpis RNA libraries confirmed the high prevalence of Lul-MV-1. This is the first report of a mitovirus infecting an insect host.
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17
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Chiba Y, Oiki S, Yaguchi T, Urayama SI, Hagiwara D. Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses. Virus Evol 2020; 7:veaa101. [PMID: 33505709 PMCID: PMC7816673 DOI: 10.1093/ve/veaa101] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
By identifying variations in viral RNA genomes, cutting-edge metagenome
technology has potential to reshape current concepts about the evolution of RNA
viruses. This technology, however, cannot process low-homology genomic regions
properly, leaving the true diversity of RNA viruses unappreciated. To overcome
this technological limitation, we applied an advanced method, Fragmented and
Primer-Ligated Double-stranded (ds) RNA Sequencing (FLDS), to screen RNA viruses
from 155 fungal isolates, which allowed us to obtain complete viral genomes in a
homology-independent manner. We created a high-quality catalog of 19 RNA viruses
(12 viral species) that infect Aspergillus isolates. Among
them, nine viruses were not detectable by the conventional methodology involving
agarose gel electrophoresis of dsRNA, a hallmark of RNA virus infections.
Segmented genome structures were determined in 42 per cent of the viruses. Some
RNA viruses had novel genome architectures; one contained a dual
methyltransferase domain and another had a separated RNA-dependent RNA
polymerase (RdRp) gene. A virus from a different fungal taxon
(Pyricularia) had an RdRp sequence that was separated on
different segments, suggesting that a divided RdRp is widely present among
fungal viruses, despite the belief that all RNA viruses encode RdRp as a single
gene. These findings illustrate the previously hidden diversity and evolution of
RNA viruses, and prompt reconsideration of the structural plasticity of
RdRp.
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Affiliation(s)
- 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
| | - Sayoko Oiki
- 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 Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, 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
| | - 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
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18
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Liu Y, Zhang L, Esmael A, Duan J, Bian X, Jia J, Xie J, Cheng J, Fu Y, Jiang D, Lin Y. Four Novel Botourmiaviruses Co-Infecting an Isolate of the Rice Blast Fungus Magnaporthe oryzae. Viruses 2020; 12:E1383. [PMID: 33287110 PMCID: PMC7761653 DOI: 10.3390/v12121383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
Via virome sequencing, six viruses were detected from Magnaporthe oryzae strains YC81-2, including one virus in the family Tombusviridae, one virus in the family Narnaviridae and four viruses in the family Botourmiaviridae. Since the RNA-dependent RNA polymerase (RdRp) of one botourmiavirus show the highest identity (79%) with Magnaporthe oryzae ourmia-like virus 1 (MOLV1), the virus that was grouped into the genus Magoulivirus was designated as Magnaporthe oryzae botourmiavirus 2 (MOBV2). The three other novel botourmiaviruses were selected for further study. The complete nucleotide sequences of the three botourmiaviruses were determined. Sequence analysis showed that virus 1, virus 2, and virus 3 were 2598, 2385, and 2326 nts in length, respectively. The variable 3' untranslated region (3'-UTR) and 5'-UTR of each virus could be folded into a stable stem-loop secondary structure. Each virus consisted of a unique ORF encoding a putative RdRp. The putative proteins with a conserved GDD motif of RdRp showed the highest sequence similarity to RdRps of viruses in the family Botourmiaviridae. Phylogenetic analysis demonstrated that these viruses were three distinct novel botourmiaviruses, clustered into the Botourmiaviridae family but not belonging to any known genera of this family. Thus, virus 1, virus 2, and virus 3 were designated as Magnaporthe oryzae botourmiavirus 5, 6, and 7 (MOBV5, MOBV6, and MOBV7), respectively. Our results suggest that four distinct botourmiaviruses, MOBV2, MOBV5, MOBV6, and MOBV7, co-infect a single strain of Magnaporthe oryzae, and MOBV5, MOBV6, and MOBV7 are members of three unclassified genera in the family Botourmiaviridae.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
| | - Liyan Zhang
- Institute of Biotechnology, Heilongjiang Academy of Agricultural Sciences, Harbin 150001, China;
| | - Ahmed Esmael
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
- Botany and Microbiology Department, Faculty of Science, Benha University, Qalubiya Governorate, Benha 13511, Egypt
| | - Jie Duan
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Xuefeng Bian
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Jiasen Cheng
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Yang Lin
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
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Chiapello M, Rodríguez-Romero J, Ayllón MA, Turina M. Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages. Virus Evol 2020; 6:veaa058. [PMID: 33324489 PMCID: PMC7724247 DOI: 10.1093/ve/veaa058] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The obligatory biotrophic oomycetes Plasmopara viticola is the causal agent of downy mildew, a destructive disease of grapevine worldwide. So far, chemical fungicides are widely employed to limit this pathogen, but their adverse effects are stimulating the quest for environmentally friendly alternative approaches. Here, we report on the search for mycoviruses that might be later developed as biocontrol agents for this pathogen. Symptomatic leaves were collected from various regions in Spain and Italy and mycelia associated to leaf lesions was harvested. Total RNA extractions were depleted of rRNA and metatranscriptomes were generated using a high-throughput sequencing approach. The virome associated to leaf lesions was then characterized through a bioinformatic pipeline relying on blast searches against current viral databases. Here, we present an inventory of 283 new RNA viruses: 222 positive strand RNA viruses, 29 negative strand RNA viruses, 27 double-stranded RNA viruses and 5 ORFan virus RdRP segments, which could not be reliably assigned to any existing group in the Riboviria. In addition to ORFan viruses, we found other surprising new evolutionary trajectories in this wide inventory of viruses. The most represented viruses in our collection are those in phylum Lenarviricota, and, among them, a group of mycovirus segments distantly related to narnaviruses, but characterized by a polymerase palm domain lacking subdomain C, with the putative GDD catalytic triad. We also provided evidence of a strict association between two RNA segments that form a new mycovirus clade of positive strand RNA in the phylum Kitrinoviricota, order Martellivirales. In the phylum Negarnaviricota, we report for the first time in the order Mononegavirales a clade of viruses that is ambisense, a feature that so far was present only in the order Bunyavirales. Furthermore, in the same phylum we detected the widespread occurrence and abundant accumulation in our libraries of a distinct mycovirus clade distantly related to the Muvirales and Goujanvirales orders, which so far include only viruses infecting invertebrates. Possible new oomycetes-specific virus clades are also described in the phylum Duplornaviricota. These data greatly expand the evolutionary history of mycoviruses adding new layers of diversity to the realm Riboviria.
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Affiliation(s)
- M Chiapello
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - J Rodríguez-Romero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid 28040, Spain
| | - M A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid 28040, Spain
| | - M Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
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Owashi Y, Aihara M, Moriyama H, Arie T, Teraoka T, Komatsu K. Population Structure of Double-Stranded RNA Mycoviruses That Infect the Rice Blast Fungus Magnaporthe oryzae in Japan. Front Microbiol 2020; 11:593784. [PMID: 33193269 PMCID: PMC7664462 DOI: 10.3389/fmicb.2020.593784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/28/2020] [Indexed: 11/28/2022] Open
Abstract
Various viruses infect Magnaporthe oryzae (syn. Pyricularia oryzae), which is a well-studied fungus that causes rice blast disease. Most research has focused on the discovery of new viruses and the hypovirulence-associated traits conferred by them. Therefore, the diversity and prevalence of viruses in wild fungal populations have not been explored. We conducted a comprehensive screening of M. oryzae mycoviruses from various regions in Japan using double-stranded RNA (dsRNA) electrophoresis and RT-PCR assays. We detected three mycoviruses, Magnaporthe oryzae virus 2 (MoV2), Magnaporthe oryzae chrysovirus 1 (MoCV1), and Magnaporthe oryzae partitivirus 1 (MoPV1), among 127 of the 194 M. oryzae strains screened. The most prevalent virus was MoPV1 (58.8%), which often co-infected in a single fungal strain together with MoV2 or MoCV1. MoV2 and MoCV1 were found in 22.7 and 10.8% of strains, respectively, and they were usually distributed in different regions so that mixed-infection with these two mycoviruses was extremely rare. The predominance of MoPV1 in M. oryzae is supported by significant negative values from neutrality tests, which indicate that the population size of MoPV1 tends to increase. Population genetic analyses revealed high nucleotide diversity and the presence of phylogenetically diverse subpopulations among the MoV2 isolates. This was not the case for MoPV1. Furthermore, studies of a virus-cured M. oryzae strain revealed that MoV2 does not cause any abnormalities or symptoms in its host. However, a leaf sheath inoculation assay showed that its presence slightly increased the speed of mycelial growth, compared with virus-free mycelia. These results demonstrate that M. oryzae in Japan harbors diverse dsRNA mycovirus communities with wide variations in their population structures among different viruses.
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Affiliation(s)
- Yuta Owashi
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan.,Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Mitsuhiro Aihara
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Hiromitsu Moriyama
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Tohru Teraoka
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Japan
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Sutela S, Forgia M, Vainio EJ, Chiapello M, Daghino S, Vallino M, Martino E, Girlanda M, Perotto S, Turina M. The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization. Virus Evol 2020; 6:veaa076. [PMID: 33324490 PMCID: PMC7724248 DOI: 10.1093/ve/veaa076] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutualistic plant-associated fungi are recognized as important drivers in plant evolution, diversity, and health. The discovery that mycoviruses can take part and play important roles in symbiotic tripartite interactions has prompted us to study the viromes associated with a collection of ericoid and orchid mycorrhizal (ERM and ORM, respectively) fungi. Our study, based on high-throughput sequencing of transcriptomes (RNAseq) from fungal isolates grown in axenic cultures, revealed in both ERM and ORM fungi the presence of new mycoviruses closely related to already classified virus taxa, but also new viruses that expand the boundaries of characterized RNA virus diversity to previously undescribed evolutionary trajectories. In ERM fungi, we provide first evidence of a bipartite virus, distantly related to narnaviruses, that splits the RNA-dependent RNA polymerase (RdRP) palm domain into two distinct proteins, encoded by each of the two segments. Furthermore, in one isolate of the ORM fungus Tulasnella spp. we detected a 12 kb genomic fragment coding for an RdRP with features of bunyavirus-like RdRPs. However, this 12 kb genomic RNA has the unique features, for Bunyavirales members, of being tri-cistronic and carrying ORFs for the putative RdRP and putative nucleocapsid in ambisense orientation on the same genomic RNA. Finally, a number of ORM fungal isolates harbored a group of ambisense bicistronic viruses with a genomic size of around 5 kb, where we could identify a putative RdRP palm domain that has some features of plus strand RNA viruses; these new viruses may represent a new lineage in the Riboviria, as they could not be reliably assigned to any of the branches in the recently derived monophyletic tree that includes most viruses with an RNA genome.
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Affiliation(s)
- Suvi Sutela
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity Group, Latokartanonkaari 9, Helsinki FI-00790, Finland
| | - Marco Forgia
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Eeva J Vainio
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity Group, Latokartanonkaari 9, Helsinki FI-00790, Finland
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Stefania Daghino
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Elena Martino
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Mariangela Girlanda
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Silvia Perotto
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
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