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Urzo MLR, Guinto TD, Eusebio-Cope A, Budot BO, Yanoria MJT, Jonson GB, Arakawa M, Kondo H, Suzuki N. Metatranscriptomic Sequencing of Sheath Blight-Associated Isolates of Rhizoctonia solani Revealed Multi-Infection by Diverse Groups of RNA Viruses. Viruses 2024; 16:1152. [PMID: 39066314 DOI: 10.3390/v16071152] [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: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Rice sheath blight, caused by the soil-borne fungus Rhizoctonia solani (teleomorph: Thanatephorus cucumeris, Basidiomycota), is one of the most devastating phytopathogenic fungal diseases and causes yield loss. Here, we report on a very high prevalence (100%) of potential virus-associated double-stranded RNA (dsRNA) elements for a collection of 39 fungal strains of R. solani from the rice sheath blight samples from at least four major rice-growing areas in the Philippines and a reference isolate from the International Rice Research Institute, showing different colony phenotypes. Their dsRNA profiles suggested the presence of multiple viral infections among these Philippine R. solani populations. Using next-generation sequencing, the viral sequences of the three representative R. solani strains (Ilo-Rs-6, Tar-Rs-3, and Tar-Rs-5) from different rice-growing areas revealed the presence of at least 36 viruses or virus-like agents, with the Tar-Rs-3 strain harboring the largest number of viruses (at least 20 in total). These mycoviruses or their candidates are believed to have single-stranded RNA or dsRNA genomes and they belong to or are associated with the orders Martellivirales, Hepelivirales, Durnavirales, Cryppavirales, Ourlivirales, and Ghabrivirales based on their coding-complete RNA-dependent RNA polymerase sequences. The complete genome sequences of two novel RNA viruses belonging to the proposed family Phlegiviridae and family Mitoviridae were determined.
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Affiliation(s)
- Michael Louie R Urzo
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Timothy D Guinto
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Ana Eusebio-Cope
- Fit-for-Future Genetic Resources Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Bernard O Budot
- Institute of Weed Science, Entomology, and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Mary Jeanie T Yanoria
- Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Gilda B Jonson
- Traits for Challenged Environments Unit, Rice Breeding Innovations Department, International Rice Research Institute (IRRI), University of the Philippines Los Baños, Los Baños 4031, Laguna, Philippines
| | - Masao Arakawa
- Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
| | - Hideki Kondo
- Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Plant-Microbe Interactions Group, Institute of Plant Science and Resources (IPSR), Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan
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Fan Y, Zhao W, Tang X, Wang L, Yang M, Yang Y, Cheng B, Zhou E, He Z. Characterization of a novel gammapartitivirus infecting the phytopathogenic fungus Pyricularia oryzae. Arch Virol 2024; 169:105. [PMID: 38637359 DOI: 10.1007/s00705-024-06031-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/16/2024] [Indexed: 04/20/2024]
Abstract
In this study, we identified a novel double-strand RNA (dsRNA) mycovirus in Pyricularia oryzae, designated "Magnaporthe oryzae partitivirus 4" (MoPV4). The genome of MoPV4 consists of a dsRNA-1 segment encoding an RNA-dependent RNA polymerase (RdRP) and a dsRNA-2 segment encoding a capsid protein (CP). Phylogenetic analysis indicated that MoPV4 belongs to the genus Gammapartitivirus within family Partitiviridae. The particles of MoPV4 are isometric with a diameter of about 32.4 nm. Three-dimensional structure predictions indicated that the RdRP of MoPV4 forms a classical right-handed conformation, while the CP has a reclining-V shape.
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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, 510642, Guangzhou, China
| | - Wenhua Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, 510642, Guangzhou, China
| | - XiaoLin Tang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, 510642, Guangzhou, China
| | - Li Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, 510642, Guangzhou, China
| | - Mei Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, 510642, Guangzhou, China
| | - Yingqing Yang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Baoping Cheng
- Institute of Plant Protection, 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 Academy of Agricultural Sciences, 510642, Guangdong, China.
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, 510642, Guangzhou, China.
| | - Zhenrui He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, 510642, Guangzhou, China.
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Sun A, Zhao L, Sun Y, Chen Y, Li C, Dong W, Yang G. Horizontal and Vertical Transmission of a Mycovirus Closely Related to the Partitivirus RhsV717 That Confers Hypovirulence in Rhizoctonia solani. Viruses 2023; 15:2088. [PMID: 37896865 PMCID: PMC10611285 DOI: 10.3390/v15102088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Rhizoctonia solani virus717 (RhsV717) was isolated from the Rhizoctonia solani (R. solani) AG-2 strain Rhs717. This study isolated a virus designated as Rhizoctonia solani partitivirus BS-5 (RsPV-BS5) from the R. solani AG-3 strain BS-5, the causal agent of tobacco target spot disease. The virus was identified as a strain of RhsV717. Transmission electron microscopy (TEM) images showed that RsPV-BS5 had virus particles with a diameter of approximately 40 nm. Importantly, it can be horizontally transmitted through hyphal anastomosis and vertically transmitted via sexual basidiospores. Furthermore, this study demonstrated that RsPV-BS5 infection significantly impedes mycelial growth and induces hypovirulence in tobacco leaves. Thus, RsPV-BS5 presents a promising avenue for biocontrolling tobacco target spot disease. Transcriptome analysis unveiled differential expression of four genes related to cell wall-degrading enzymes between two isogenic strains, 06-2-15V and 06-2-15. These findings shed light on the molecular mechanism through which RsPV-BS5 reduces host pathogenicity.
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Affiliation(s)
- Aili Sun
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (A.S.); (L.Z.); (Y.S.); (Y.C.); (C.L.)
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650000, China
| | - Lianjing Zhao
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (A.S.); (L.Z.); (Y.S.); (Y.C.); (C.L.)
| | - Yang Sun
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (A.S.); (L.Z.); (Y.S.); (Y.C.); (C.L.)
| | - Yingrui Chen
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (A.S.); (L.Z.); (Y.S.); (Y.C.); (C.L.)
| | - Chengyun Li
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (A.S.); (L.Z.); (Y.S.); (Y.C.); (C.L.)
| | - Wenhan Dong
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (A.S.); (L.Z.); (Y.S.); (Y.C.); (C.L.)
| | - Genhua Yang
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (A.S.); (L.Z.); (Y.S.); (Y.C.); (C.L.)
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Liu C, Jiang X, Tan Z, Wang R, Shang Q, Li H, Xu S, Aranda MA, Wu B. An Outstandingly Rare Occurrence of Mycoviruses in Soil Strains of the Plant-Beneficial Fungi from the Genus Trichoderma and a Novel Polymycoviridae Isolate. Microbiol Spectr 2023; 11:e0522822. [PMID: 37022156 PMCID: PMC10269472 DOI: 10.1128/spectrum.05228-22] [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: 12/24/2022] [Accepted: 01/31/2023] [Indexed: 04/07/2023] Open
Abstract
In fungi, viral infections frequently remain cryptic causing little or no phenotypic changes. It can indicate either a long history of coevolution or a strong immune system of the host. Some fungi are outstandingly ubiquitous and can be recovered from a great diversity of habitats. However, the role of viral infection in the emergence of environmental opportunistic species is not known. The genus of filamentous and mycoparasitic fungi Trichoderma (Hypocreales, Ascomycota) consists of more than 400 species, which mainly occur on dead wood, other fungi, or as endo- and epiphytes. However, some species are environmental opportunists because they are cosmopolitan, can establish in a diversity of habitats, and can also become pests on mushroom farms and infect immunocompromised humans. In this study, we investigated the library of 163 Trichoderma strains isolated from grassland soils in Inner Mongolia, China, and found only four strains with signs of the mycoviral nucleic acids, including a strain of T. barbatum infected with a novel strain of the Polymycoviridae and named and characterized here as Trichoderma barbatum polymycovirus 1 (TbPMV1). Phylogenetic analysis suggested that TbPMV1 was evolutionarily distinct from the Polymycoviridae isolated either from Eurotialean fungi or from the order Magnaportales. Although the Polymycoviridae viruses were also known from Hypocrealean Beauveria bassiana, the phylogeny of TbPMV1 did not reflect the phylogeny of the host. Our analysis lays the groundwork for further in-depth characterization of TbPMV1 and the role of mycoviruses in the emergence of environmental opportunism in Trichoderma. IMPORTANCE Although viruses infect all organisms, our knowledge of some groups of eukaryotes remains limited. For instance, the diversity of viruses infecting fungi-mycoviruses-is largely unknown. However, the knowledge of viruses associated with industrially relevant and plant-beneficial fungi, such as Trichoderma spp. (Hypocreales, Ascomycota), may shed light on the stability of their phenotypes and the expression of beneficial traits. In this study, we screened the library of soilborne Trichoderma strains because these isolates may be developed into bioeffectors for plant protection and sustainable agriculture. Notably, the diversity of endophytic viruses in soil Trichoderma was outstandingly low. Only 2% of 163 strains contained traces of dsRNA viruses, including the new Trichoderma barbatum polymycovirus 1 (TbPMV1) characterized in this study. TbPMV1 is the first mycovirus found in Trichoderma. Our results indicate that the limited data prevent the in-depth study of the evolutionary relationship between soilborne fungi and is worth further investigation.
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Affiliation(s)
- Chenchen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiliang Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaoyan Tan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rongqun Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoxia Shang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
| | - Hongrui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture and Landscapes, Tianjin Agricultural University, Tianjin, China
| | - Shujin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture and Landscapes, Tianjin Agricultural University, Tianjin, China
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Murcia, Spain
| | - Beilei Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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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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Metatranscriptomic Analysis Reveals Rich Mycoviral Diversity in Three Major Fungal Pathogens of Rice. Int J Mol Sci 2022; 23:ijms23169192. [PMID: 36012458 PMCID: PMC9409214 DOI: 10.3390/ijms23169192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, three major fungal diseases of rice, i.e., rice blast, rice false smut, and rice-sheath blight, have caused serious worldwide rice-yield reductions and are threatening global food security. Mycoviruses are ubiquitous in almost all major groups of filamentous fungi, oomycetes, and yeasts. To reveal the mycoviral diversity in three major fungal pathogens of rice, we performed a metatranscriptomic analysis of 343 strains, representing the three major fungal pathogens of rice, Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, sampled in southern China. The analysis identified 682 contigs representing the partial or complete genomes of 68 mycoviruses, with 42 described for the first time. These mycoviruses showed affinity with eight distinct lineages: Botourmiaviridae, Partitiviridae, Totiviridae, Chrysoviridae, Hypoviridae, Mitoviridae, Narnaviridae, and Polymycoviridae. More than half (36/68, 52.9%) of the viral sequences were predicted to be members of the families Narnaviridae and Botourmiaviridae. The members of the family Polymycoviridae were also identified for the first time in the three major fungal pathogens of rice. These findings are of great significance for understanding the diversity, origin, and evolution of, as well as the relationship between, genome structures and functions of mycoviruses in three major fungal pathogens of rice.
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