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Hai D, Li J, Jiang D, Cheng J, Fu Y, Xiao X, Yin H, Lin Y, Chen T, Li B, Yu X, Cai Q, Chen W, Kotta-Loizou I, Xie J. Plants interfere with non-self recognition of a phytopathogenic fungus via proline accumulation to facilitate mycovirus transmission. Nat Commun 2024; 15:4748. [PMID: 38834585 DOI: 10.1038/s41467-024-49110-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
Non-self recognition is a fundamental aspect of life, serving as a crucial mechanism for mitigating proliferation of molecular parasites within fungal populations. However, studies investigating the potential interference of plants with fungal non-self recognition mechanisms are limited. Here, we demonstrate a pronounced increase in the efficiency of horizontal mycovirus transmission between vegetatively incompatible Sclerotinia sclerotiorum strains in planta as compared to in vitro. This increased efficiency is associated with elevated proline concentration in plants following S. sclerotiorum infection. This surge in proline levels attenuates the non-self recognition reaction among fungi by inhibition of cell death, thereby facilitating mycovirus transmission. Furthermore, our field experiments reveal that the combined deployment of hypovirulent S. sclerotiorum strains harboring hypovirulence-associated mycoviruses (HAVs) together with exogenous proline confers substantial protection to oilseed rape plants against virulent S. sclerotiorum. This unprecedented discovery illuminates a novel pathway by which plants can counteract S. sclerotiorum infection, leveraging the weakening of fungal non-self recognition and promotion of HAVs spread. These promising insights provide an avenue to explore for developing innovative biological control strategies aimed at mitigating fungal diseases in plants by enhancing the efficacy of horizontal HAV transmission.
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Affiliation(s)
- Du Hai
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jincang Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Daohong Jiang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jiasen Cheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanping Fu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xueqiong Xiao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tao Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Bo Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Xiao Yu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Qing Cai
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Ioly Kotta-Loizou
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Jiatao Xie
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China.
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
- Hubei Hongshan Laboratory, Wuhan, Hubei, China.
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Wang X, Kotta-Loizou I, Coutts RHA, Deng H, Han Z, Hong N, Shafik K, Wang L, Guo Y, Yang M, Xu W, Wang G. A circular single-stranded DNA mycovirus infects plants and confers broad-spectrum fungal resistance. MOLECULAR PLANT 2024; 17:955-971. [PMID: 38745413 DOI: 10.1016/j.molp.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Circular single-stranded DNA (ssDNA) viruses have been rarely found in fungi, and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear. In this study, a novel circular ssDNA virus, tentatively named Diaporthe sojae circular DNA virus 1 (DsCDV1), was identified in the phytopathogenic fungus Diaporthe sojae isolated from pear trees. DsCDV1 has a monopartite genome (3185 nt in size) encapsidated in isometric virions (21-26 nm in diameter). The genome comprises seven putative open reading frames encoding a discrete replicase (Rep) split by an intergenic region, a putative capsid protein (CP), several proteins of unknown function (P1-P4), and a long intergenic region. Notably, the two split parts of DsCDV1 Rep share high identities with the Reps of Geminiviridae and Genomoviridae, respectively, indicating an evolutionary linkage with both families. Phylogenetic analysis based on Rep or CP sequences placed DsCDV1 in a unique cluster, supporting the establishment of a new family, tentatively named Gegemycoviridae, intermediate to both families. DsCDV1 significantly attenuates fungal growth and nearly erases fungal virulence when transfected into the host fungus. Remarkably, DsCDV1 can systematically infect tobacco and pear seedlings, providing broad-spectrum resistance to fungal diseases. Subcellular localization analysis revealed that DsCDV1 P3 is systematically localized in the plasmodesmata, while its expression in trans-complementation experiments could restore systematic infection of a movement-deficient plant virus, suggesting that P3 is a movement protein. DsCDV1 exhibits unique molecular and biological traits not observed in other ssDNA viruses, serving as a link between fungal and plant ssDNA viruses and presenting an evolutionary connection between ssDNA viruses and fungi. These findings contribute to expanding our understanding of ssDNA virus diversity and evolution, offering potential biocontrol applications for managing crucial plant diseases.
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Affiliation(s)
- Xianhong Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK; Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Robert H A Coutts
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Huifang Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Zhenhao Han
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Karim Shafik
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China; Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria 21526, Egypt
| | - Liping Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Yashuang Guo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Mengmeng Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Wenxing Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China.
| | - Guoping Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China.
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Jia J, Nan L, Song Z, Chen X, Xia J, Cheng L, Zhang B, Mu F. Cross-species transmission of a novel bisegmented orfanplasmovirus in the phytopathogenic fungus Exserohilum rostratum. Front Microbiol 2024; 15:1409677. [PMID: 38846572 PMCID: PMC11153860 DOI: 10.3389/fmicb.2024.1409677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Mycoviruses have been found in various fungal species across different taxonomic groups, while no viruses have been reported yet in the fungus Exserohilum rostratum. In this study, a novel orfanplasmovirus, namely Exserohilum rostratum orfanplasmovirus 1 (ErOrfV1), was identified in the Exserohilum rostratum strain JZ1 from maize leaf. The complete genome of ErOrfV1 consists of two positive single-stranded RNA segments, encoding an RNA-dependent RNA polymerase and a hypothetical protein with unknown function, respectively. Phylogenetic analysis revealed that ErOrfV1 clusters with other orfanplasmoviruses, forming a distinct phyletic clade. A new family, Orfanplasmoviridae, is proposed to encompass this newly discovered ErOrfV1 and its associated orfanplasmoviruses. ErOrfV1 exhibits effective vertical transmission through conidia, as evidenced by its 100% presence in over 200 single conidium isolates. Moreover, it can be horizontally transmitted to Exserohilum turcicum. Additionally, the infection of ErOrfV1 is cryptic in E. turcicum because there were no significant differences in mycelial growth rate and colony morphology between ErOrfV1-infected and ErOrfV1-free strains. This study represents the inaugural report of a mycovirus in E. rostratum, as well as the first documentation of the biological and transmission characteristics of orfanplasmovirus. These discoveries significantly contribute to our understanding of orfanplasmovirus.
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Affiliation(s)
- Jichun Jia
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Linjie Nan
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Zehao Song
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Xu Chen
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Jinsheng Xia
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Lihong Cheng
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Baojun Zhang
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Fan Mu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
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Sadiq S, Harvey E, Mifsud JCO, Minasny B, McBratney AB, Pozza LE, Mahar JE, Holmes EC. Australian terrestrial environments harbour extensive RNA virus diversity. Virology 2024; 593:110007. [PMID: 38346363 DOI: 10.1016/j.virol.2024.110007] [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: 10/11/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2460 putatively novel RNA viruses across 18 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota. In many orders, such as the Nodamuvirales and Ghabrivirales, the novel viruses identified here comprised entirely new clades. Novel viruses also fell between established genera or families, such as in the Cystoviridae and Picornavirales, while highly divergent lineages were identified in the Sobelivirales and Ghabrivirales. Viral read abundance and alpha diversity were influenced by sampling site, soil type and land use, but not by depth from the surface. In sum, Australian soils and sediments are home to remarkable viral diversity, reflecting the biodiversity of local fauna and flora.
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Affiliation(s)
- Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alex B McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liana E Pozza
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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Zhang C, Zheng X, Tie Z, Xi H, Shi M, Ma Y, Chen W, Mi Y, Yang R, Zhao S, Zhang X. Identification of Mycoviruses in the Pathogens of Fragrant Pear Valsa Canker from Xinjiang in China. Viruses 2024; 16:355. [PMID: 38543721 PMCID: PMC10974596 DOI: 10.3390/v16030355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 05/23/2024] Open
Abstract
As a common disease, canker seriously affects the yield and quality of fragrant pear due to the lack of effective control measures. Some fungi have been reported to harbor rich reservoirs of viral resources, and some mycoviruses can be used as biocontrol agents against plant diseases. In this study, 199 isolates were obtained from diseased branches of fragrant pear in the main production areas of Xinjiang. Among them, 134 belonged to Valsa spp., identified using morphological and molecular biological techniques, in which V. mali was the dominant species. The mycoviruses in Valsa spp. were further identified using metatranscriptomic sequencing and RT-PCR. The results revealed that a total of seven mycoviruses were identified, belonging to Botourmiaviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mitoviridae, and Narnaviridae, among which Phomopsis longicolla hypovirus (PlHV) was dominant in all the sample collection regions. The Cryphonectria hypovirus 3-XJ1 (CHV3-XJ1), Botourmiaviridae sp.-XJ1 (BVsp-XJ1), and Fusariviridae sp.-XJ1 (Fvsp-XJ1) were new mycoviruses discovered within the Valsa spp. More importantly, compared with those in the virus-free Valsa spp. strain, the growth rate and virulence of the VN-5 strain co-infected with PlHV and CHV3-XJ1 were reduced by 59% and 75%, respectively, and the growth rate and virulence of the VN-34 strain infected with PlHV were reduced by 42% and 55%, respectively. On the other hand, the horizontal transmission efficiency of PlHV decreased when PlHV was co-infected with CHV3-XJ1, indicating that PlHV and CHV3-XJ1 were antagonistic. In summary, the mycoviruses in Valsa spp. were identified in Xinjiang for the first time, and three of them were newly discovered mycoviruses, with two strains yielding good results. These results will offer potential biocontrol resources for managing pear canker disease and provide a theoretical basis for the control of fruit tree Valsa canker disease.
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Affiliation(s)
- Chenguang Zhang
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Xiaoya Zheng
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Zhanjiang Tie
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Hui Xi
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Mai Shi
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Yanjun Ma
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Wenbin Chen
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Yingjie Mi
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Rui Yang
- Agricultural Technology Extension Station of the First Division, Alaer 843300, China;
| | - Sifeng Zhao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
| | - Xuekun Zhang
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, College of Agriculture, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (C.Z.); (X.Z.); (Z.T.); (H.X.); (M.S.); (Y.M.); (W.C.); (Y.M.)
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Ma K, Cai L, Wang R, Wang J, Zhan H, Ni H, Lu B, Zhang Y, Gao J. Complete genome sequence of a novel mitovirus isolated from the fungus Fusarium oxysporum f. sp. ginseng causing ginseng root rot. Arch Virol 2024; 169:53. [PMID: 38381240 DOI: 10.1007/s00705-024-05962-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 02/22/2024]
Abstract
A novel mitovirus, tentatively designated as "Fusarium oxysporum mitovirus 2" (FoMV2), was isolated from the pathogenic Fusarium oxysporum f. sp. ginseng strain 0414 infecting Panax ginseng. The complete genome of FoMV2 is 2388 nt in length with a GC content of 30.57%. It contains a large open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) of 713 amino acids with a molecular weight of 83.05 kDa. The sequence identity between FoMV2 and Botrytis cinerea mitovirus 8 and Fusarium verticillioides mitovirus 1 was 87.94% and 77.85%, respectively. Phylogenetic analysis showed that FoMV2 belongs to the genus Unuamitovirus in the family Mitoviridae. To the best of our knowledge, this is the first report of an unuamitovirus isolated from F. oxysporum f. sp. ginseng causing ginseng root rot.
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Affiliation(s)
- Kaige Ma
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Liping Cai
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Ruojin Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Jun Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Haoxin Zhan
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Hechi Ni
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Baohui Lu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China
| | - Yanjing Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China.
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China.
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Li S, Ma Z, Zhang X, Cai Y, Han C, Wu X. Sixteen Novel Mycoviruses Containing Positive Single-Stranded RNA, Double-Stranded RNA, and Negative Single-Stranded RNA Genomes Co-Infect a Single Strain of Rhizoctonia zeae. J Fungi (Basel) 2023; 10:30. [PMID: 38248940 PMCID: PMC10817634 DOI: 10.3390/jof10010030] [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: 10/06/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
In the present study, sixteen novel RNA mycoviruses co-infecting a single strain of Rhizoctonia zeae (strain D40) were identified and molecularly characterized using metatranscriptome sequencing combined with a method for rapid amplification of cDNA ends. The fungal strain was isolated from diseased seedlings of sugar beet with damping-off symptoms. Based on genome analysis and phylogenetic analysis of amino acid sequences of RNA-dependent RNA polymerase, the sixteen mycoviruses associated with strain D40 contained three genome types with nine distinct lineages, including positive single-stranded RNA (Hypoviridae, Yadokariviridae, Botourmiaviridae, and Gammaflexiviridae), double-stranded RNA (Phlegiviridae, Megabirnaviridae, Megatotiviridae, and Yadonushiviridae), and negative single-stranded RNA (Tulasviridae), suggesting a complex composition of a mycoviral community in this single strain of R. zeae (strain D40). Full genome sequences of six novel mycoviruses and the nearly full-length sequences of the remaining ten novel mycoviruses were obtained. Furthermore, seven of these sixteen mycoviruses were confirmed to assemble virus particles present in the R. zeae strain D40. To the best of our knowledge, this is the first detailed study of mycoviruses infecting R. zeae.
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Affiliation(s)
| | | | | | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China; (S.L.); (Z.M.); (X.Z.); (Y.C.); (C.H.)
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8
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Contreras-Soto MB, Tovar-Pedraza JM. Viruses of plant-pathogenic fungi: a promising biocontrol strategy for Sclerotinia sclerotiorum. Arch Microbiol 2023; 206:38. [PMID: 38142438 DOI: 10.1007/s00203-023-03774-8] [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: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/26/2023]
Abstract
Plant pathogenic fungi pose a significant and ongoing threat to agriculture and food security, causing economic losses and significantly reducing crop yields. Effectively managing these fungal diseases is crucial for sustaining agricultural productivity, and in this context, mycoviruses have emerged as a promising biocontrol option. These viruses alter the physiology of their fungal hosts and their interactions with the host plants. This review encompasses the extensive diversity of reported mycoviruses, including their taxonomic classification and range of fungal hosts. We highlight representative examples of mycoviruses that affect economically significant plant-pathogenic fungi and their distinctive characteristics, with a particular emphasis on mycoviruses impacting Sclerotinia sclerotiorum. These mycoviruses exhibit significant potential for biocontrol, supported by their specificity, efficacy, and environmental safety. This positions mycoviruses as valuable tools in crop protection against diseases caused by this pathogen, maintaining their study and application as promising research areas in agricultural biotechnology. The remarkable diversity of mycoviruses, coupled with their ability to infect a broad range of plant-pathogenic fungi, inspires optimism, and suggests that these viruses have the potential to serve as an effective management strategy against major fungi-causing plant diseases worldwide.
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Affiliation(s)
- María Belia Contreras-Soto
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, 80110, Culiacán, Sinaloa, Mexico
| | - Juan Manuel Tovar-Pedraza
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, 80110, Culiacán, Sinaloa, Mexico.
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9
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Khan HA, Mukhtar M, Bhatti MF. Mycovirus-induced hypovirulence in notorious fungi Sclerotinia: a comprehensive review. Braz J Microbiol 2023; 54:1459-1478. [PMID: 37523037 PMCID: PMC10485235 DOI: 10.1007/s42770-023-01073-4] [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: 04/21/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
Members of the genus Sclerotinia are notorious plant pathogens with a diverse host range that includes many important crops. A huge number of mycoviruses have been identified in this genus; some of these viruses are reported to have a hypovirulent effect on the fitness of their fungal hosts. These mycoviruses are important to researchers from a biocontrol perspective which was first implemented against fungal diseases in 1990. In this review, we have presented the data of all hypovirulent mycoviruses infecting Sclerotinia sclerotiorum isolates. The data of hypovirulent mycoviruses ranges from 1992 to 2023. Currently, mycoviruses belonging to 17 different families, including (+) ssRNA, (-ssRNA), dsRNA, and ssDNA viruses, have been reported from this genus. Advances in studies had shown a changed expression of certain host genes (responsible for cell cycle regulation, DNA replication, repair pathways, ubiquitin proteolysis, gene silencing, methylation, pathogenesis-related, sclerotial development, carbohydrate metabolism, and oxalic acid biosynthesis) during the course of mycoviral infection, which were termed differentially expressed genes (DEGs). Together, research on fungal viruses and hypovirulence in Sclerotinia species can deepen our understanding of the cellular processes that affect how virulence manifests in these phytopathogenic fungi and increase the potential of mycoviruses as a distinct mode of biological control. Furthermore, the gathered data can also be used for in-silico analysis, which includes finding the signature sites [e.g., hypovirus papain-like protease (HPP) domain, "CCHH" motif, specific stem-loop structures, p29 motif as in CHV1, A-rich sequence, CA-rich sequences as in MoV1, GCU motif as in RnMBV1, Core motifs in hypovirus-associated RNA elements (HAREs) as in CHV1] that are possibly responsible for hypovirulence in mycoviruses.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan.
- Department of Biotechnology, University of Mianwali, Mianwali, Punjab, 42200, Pakistan.
| | - Mamuna Mukhtar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
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10
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Wu T, Mao H, Hai D, Cheng J, Fu Y, Lin Y, Jiang D, Xie J. Molecular characterization of a novel fungal alphaflexivirus reveals potential inter-species horizontal gene transfer. Virus Res 2023; 334:199151. [PMID: 37302657 PMCID: PMC10410596 DOI: 10.1016/j.virusres.2023.199151] [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: 04/26/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/13/2023]
Abstract
Sclerotinia sclerotiorum is a notorious phytopathogenic fungus that harbors diverse mycoviruses. A novel positive-sense single-stranded RNA virus, Sclerotinia sclerotiorum alphaflexivirus 2 (SsAFV2), was isolated from the hypovirulent strain 32-9 of S. sclerotiorum, and its complete genome was determined. The SsAFV2 genome contains 7,162 nucleotides (nt), excluding the poly (A) structure, and is composed of four open reading frames (ORF1-4). ORF1 encodes a polyprotein that contains three conserved domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp). The ORF3 putative encodes coat proteins (CP), with ORF2 and ORF4 encoding hypothetical proteins of unknown functions. Phylogenetic analysis revealed that SsAFV2 clustered with Botrytis virus X (BVX) based on multiple alignments of helicase, RdRp, and CP, but the methyltransferase of SsAFV2 was most closely related to Sclerotinia sclerotiorum alphaflexivirus 1, suggesting that SsAFV2 is a new member of the Botrexvirus genus within the Alphaflexiviridae family, and also revealed the occurrence of potential inter-species horizontal gene transfer events within the Botrexvirus genus during the evolutionary process. Our results contribute to the current knowledge regarding the evolution and divergence of Botrexviruses.
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Affiliation(s)
- Tun Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Huilun Mao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China; College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Du Hai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanping Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yang Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China.
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11
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Liu H, Zhang Y, Liu Y, Xiao J, Huang Z, Li Y, Li H, Li P. Virome analysis of an ectomycorrhizal fungus Suillus luteus revealing potential evolutionary implications. Front Cell Infect Microbiol 2023; 13:1229859. [PMID: 37662006 PMCID: PMC10470027 DOI: 10.3389/fcimb.2023.1229859] [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: 05/27/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Suillus luteus is a widespread edible ectomycorrhizal fungus that holds significant importance in both ecological and economic value. Mycoviruses are ubiquitous infectious agents hosted in different fungi, with some known to exert beneficial or detrimental effects on their hosts. However, mycoviruses hosted in ectomycorrhizal fungi remain poorly studied. To address this gap in knowledge, we employed next-generation sequencing (NGS) to investigate the virome of S. luteus. Using BLASTp analysis and phylogenetic tree construction, we identified 33 mycovirus species, with over half of them belonging to the phylum Lenarviricota, and 29 of these viruses were novel. These mycoviruses were further grouped into 11 lineages, with the discovery of a new negative-sense single-stranded RNA viral family in the order Bunyavirales. In addition, our findings suggest the occurrence of cross-species transmission (CST) between the fungus and ticks, shedding light on potential evolutionary events that have shaped the viral community in different hosts. This study is not only the first study to characterize mycoviruses in S. luteus but highlights the enormous diversity of mycoviruses and their implications for virus evolution.
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Affiliation(s)
| | | | | | | | | | | | - Huaping Li
- Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
| | - Pengfei Li
- Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
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12
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Pagnoni S, Oufensou S, Balmas V, Bulgari D, Gobbi E, Forgia M, Migheli Q, Turina M. A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations. Virus Evol 2023; 9:vead042. [PMID: 37692893 PMCID: PMC10491862 DOI: 10.1093/ve/vead042] [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: 04/14/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 09/12/2023] Open
Abstract
Trichoderma genus includes soil-inhabiting fungi that provide important ecosystem services in their interaction with plants and other fungi, as well as biocontrol of fungal plant diseases. A collection of Trichoderma isolates from Sardinia has been previously characterized, but here we selected 113 isolates, representatives of the collection, and characterized their viral components. We carried out high-throughput sequencing of ribosome-depleted total RNA following a bioinformatics pipeline that detects virus-derived RNA-directed RNA polymerases (RdRps) and other conserved viral protein sequences. This pipeline detected seventeen viral RdRps with two of them corresponding to viruses already detected in other regions of the world and the remaining fifteen representing isolates of new putative virus species. Surprisingly, eight of them are from new negative-sense RNA viruses, a first in the genus Trichoderma. Among them is a cogu-like virus, closely related to plant-infecting viruses. Regarding the positive-sense viruses, we report the presence of an 'ormycovirus' belonging to a recently characterized group of bisegmented single-stranded RNA viruses with uncertain phylogenetic assignment. Finally, for the first time, we report a bisegmented member of Mononegavirales which infects fungi. The proteins encoded by the second genomic RNA of this virus were used to re-evaluate several viruses in the Penicillimonavirus and Plasmopamonavirus genera, here shown to be bisegmented and encoding a conserved polypeptide that has structural conservation with the nucleocapsid domain of rhabdoviruses.
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Affiliation(s)
- Saul Pagnoni
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, via Celoria 2, Milan 20133, Italy
| | - Safa Oufensou
- Department of Agricultural Sciences and NRD—Desertification Research Center, University of Sassari, Viale Italia 39a, Sassari, Sardegna 07100, Italy
| | - Virgilio Balmas
- Department of Agricultural Sciences and NRD—Desertification Research Center, University of Sassari, Viale Italia 39a, Sassari, Sardegna 07100, Italy
| | - Daniela Bulgari
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, Brescia 25123, Italy
| | - Emanuela Gobbi
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, Brescia 25123, Italy
| | - Marco Forgia
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, Torino 10135, Italy
| | - Quirico Migheli
- Department of Agricultural Sciences and NRD—Desertification Research Center, University of Sassari, Viale Italia 39a, Sassari, Sardegna 07100, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, Torino 10135, Italy
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13
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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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Villan Larios DC, Diaz Reyes BM, Pirovani CP, Loguercio LL, Santos VC, Góes-Neto A, Fonseca PLC, Aguiar ERGR. Exploring the Mycovirus Universe: Identification, Diversity, and Biotechnological Applications. J Fungi (Basel) 2023; 9:jof9030361. [PMID: 36983529 PMCID: PMC10052124 DOI: 10.3390/jof9030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
Viruses that infect fungi are known as mycoviruses and are characterized by the lack of an extracellular phase. In recent years, the advances on nucleic acids sequencing technologies have led to a considerable increase in the number of fungi-infecting viral species described in the literature, with a special interest in assessing potential applications as fungal biocontrol agents. In the present study, we performed a comprehensive review using Scopus, Web of Science, and PubMed databases to mine mycoviruses data to explore their molecular features and their use in biotechnology. Our results showed the existence of 267 mycovirus species, of which 189 are recognized by the International Committee on Taxonomy of Viruses (ICTV). The majority of the mycoviruses identified have a dsRNA genome (38.6%), whereas the Botourmiaviridae (ssRNA+) alone represents 14% of all mycoviruses diversity. Regarding fungal hosts, members from the Sclerotinicaeae appeared as the most common species described to be infected by mycoviruses, with 16 different viral families identified so far. It is noteworthy that such results are directly associated with the high number of studies and strategies used to investigate the presence of viruses in members of the Sclerotinicaeae family. The knowledge about replication strategy and possible impact on fungi biology is available for only a small fraction of the mycoviruses studied, which is the main limitation for considering these elements potential targets for biotechnological applications. Altogether, our investigation allowed us to summarize the general characteristics of mycoviruses and their hosts, the consequences, and the implications of this knowledge on mycovirus–fungi interactions, providing an important source of information for future studies.
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Affiliation(s)
- Diana Carolina Villan Larios
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Brayan Maudiel Diaz Reyes
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Carlos Priminho Pirovani
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Leandro Lopes Loguercio
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Vinícius Castro Santos
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil;
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil;
| | - Paula Luize Camargos Fonseca
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
- Department of Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
- Correspondence: (P.L.C.F.); (E.R.G.R.A.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
- Correspondence: (P.L.C.F.); (E.R.G.R.A.)
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15
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Song X, Cao J, Xie S, Wang Y, Yin X, Guo Y, Xu C, Guo L, Wu H, Zhang M. Molecular characterization of a novel ourmia‑like virus from the phytopathogenic fungus Botryosphaeria dothidea. Arch Virol 2023; 168:106. [PMID: 36899128 DOI: 10.1007/s00705-023-05739-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023]
Abstract
Here, we describe a novel ourmia-like virus, Botryosphaeria dothidea ourmia-like virus 2 (BdOLV2), derived from the phytopathogenic fungus Botryosphaeria dothidea strain ZM180192-1 infecting maize in Henan province of China. The complete genome sequence of BdOLV2 consists of a positive-sense single-stranded RNA (+ ssRNA) segment with a length of 2,532 nucleotides (nt). The sequence contains a large open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) consisting of 605 amino acids (aa) with a molecular mass of 68.59 kDa. This RdRp protein contains eight typical conserved motifs associated with ourmia-like viruses. BLASTp analysis revealed that the RdRp protein of BdOLV2 had the highest similarity (62.10%, 58.15%, and 55.75% identity, respectively) to a virus previously identified as "Botourmiaviridae sp.", Macrophomina phaseolina ourmia-like virus 2, and Macrophomina phaseolina ourmia-like virus 2-A. Phylogenetic analysis based on the RdRp aa sequence indicated that BdOLV2 is a new member of the genus Magoulivirus in the family Botourmiaviridae.
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Affiliation(s)
- Xinzheng Song
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Jiayuan Cao
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Shunpei Xie
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Yanfen Wang
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Yashuang Guo
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Chao Xu
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, 100193, Beijing, China
| | - Haiyan Wu
- Analytical Instrument Center, Henan Agricultural University, 450002, Zhengzhou, China.
| | - Meng Zhang
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China.
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16
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Zhao YJ, Shirouzu T, Chiba Y, Hosaka K, Moriyama H, Urayama SI, Hagiwara D. Identification of novel RNA mycoviruses from wild mushroom isolates in Japan. Virus Res 2023; 325:199045. [PMID: 36681193 DOI: 10.1016/j.virusres.2023.199045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The characterization of viruses from environmental samples could aid in our understanding of their ecological significance and potential for biotechnological exploitation. While there has been much focus on pathogenic fungi or commercially cultivated mushrooms, attention to viruses from wild Basidiomycota mushrooms is lacking. Therefore, in this study, we conducted viral screening of fungal mycelia isolated from wild basidiocarps using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 51 isolates, seven isolates were detected with virus-like bands during the initial screening with AGE, but only five isolates were detected with viruses after long-term storage. Using the FLDS method, we obtained seven viral genome sequences, including five double-stranded RNA (dsRNA) viruses belonging to Partitiviridae and Curvulaviridae, one positive-sense single-stranded RNA (ssRNA) virus belonging to Endornaviridae and one negative-sense ssRNA virus belonging to Tulasviridae (Bunyavirales). All viruses characterized in this study are novel species. These findings greatly expanded our knowledge of the diversity of RNA viruses from environmental samples.
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Affiliation(s)
- Yan-Jie Zhao
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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17
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Huang H, Hua X, Pang X, Zhang Z, Ren J, Cheng J, Fu Y, Xiao X, Lin Y, Chen T, Li B, Liu H, Jiang D, Xie J. Discovery and Characterization of Putative Glycoprotein-Encoding Mycoviruses in the Bunyavirales. J Virol 2023; 97:e0138122. [PMID: 36625579 PMCID: PMC9888262 DOI: 10.1128/jvi.01381-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Although segmented negative-sense RNA viruses (SNSRVs) have been frequently discovered in various fungi, most SNSRVs reported only the large segments. In this study, we investigated the diversity of the mycoviruses in the phytopathogenic fungus Fusarium asiaticum using the metatranscriptomic technique. We identified 17 fungal single-stranded RNA (ssRNA) viruses including nine viruses within Mitoviridae, one each in Narnaviridae, Botourmiaviridae, Hypoviridae, Fusariviridae, and Narliviridae, two in Mymonaviridae, and one trisegmented virus temporarily named Fusarium asiaticum mycobunyavirus 1 (FaMBV1). The FaMBV1 genome comprises three RNA segments, large (L), medium (M), and small (S) with 6,468, 2,639, and 1,420 nucleotides, respectively. These L, M, and S segments putatively encode the L protein, glycoprotein, and nucleocapsid, respectively. Phylogenetic analysis based on the L protein showed that FaMBV1 is phylogenetically clustered with Alternaria tenuissima negative-stranded RNA virus 2 (AtNSRV2) and Sclerotinia sclerotiorum negative-stranded RNA virus 5 (SsNSRV5) but distantly related to the members of the family Phenuiviridae. FaMBV1 could be vertically transmitted by asexual spores with lower efficiency (16.7%, 2/42). Comparison between FaMBV1-free and -infected fungal strains revealed that FaMBV1 has little effect on hyphal growth, pathogenicity, and conidium production, and its M segment is dispensable for viral replication and lost during subculture and asexual conidiation. The M and S segments of AtNSRV2 and SsNSRV5 were found using bioinformatics methods, indicating that the two fungal NSRVs harbor trisegmented genomes. Our results provide a new example of the existence and evolution of the segmented negative-sense RNA viruses in fungi. IMPORTANCE Fungal segmented negative-sense RNA viruses (SNSRVs) have been frequently found. Only the large segment encoding RNA-dependent RNA polymerase (RdRp) has been reported in most fungal SNSRVs, except for a few fungal SNSRVs reported to encode nucleocapsids, nonstructural proteins, or movement proteins. Virome analysis of the Fusarium spp. that cause Fusarium head blight discovered a novel virus, Fusarium asiaticum mycobunyavirus 1 (FaMBV1), representing a novel lineage of the family Phenuiviridae. FaMBV1 harbors a trisegmented genome that putatively encodes RdRp, glycoproteins, and nucleocapsids. The putative glycoprotein was first described in fungal SNSRVs and shared homology with glycoprotein of animal phenuivirus but was dispensable for its replication in F. asiaticum. Two other trisegmented fungal SNSRVs that also encode glycoproteins were discovered, implying that three-segment bunyavirus infections may be common in fungi. These findings provide new insights into the ecology and evolution of SNSRVs, particularly those infecting fungi.
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Affiliation(s)
- Huang Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Xiangmin Hua
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Xidan Pang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Zhongmei Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jingyi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
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18
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Viral cross-class transmission results in disease of a phytopathogenic fungus. THE ISME JOURNAL 2022; 16:2763-2774. [PMID: 36045287 PMCID: PMC9428384 DOI: 10.1038/s41396-022-01310-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 12/15/2022]
Abstract
Interspecies transmission of viruses is a well-known phenomenon in animals and plants whether via contacts or vectors. In fungi, interspecies transmission between distantly related fungi is often suspected but rarely experimentally documented and may have practical implications. A newly described double-strand RNA (dsRNA) virus found asymptomatic in the phytopathogenic fungus Leptosphaeria biglobosa of cruciferous crops was successfully transmitted to an evolutionarily distant, broad-host range pathogen Botrytis cinerea. Leptosphaeria biglobosa botybirnavirus 1 (LbBV1) was characterized in L. biglobosa strain GZJS-19. Its infection in L. biglobosa was asymptomatic, as no significant differences in radial mycelial growth and pathogenicity were observed between LbBV1-infected and LbBV1-free strains. However, cross-species transmission of LbBV1 from L. biglobosa to infection in B. cinerea resulted in the hypovirulence of the recipient B. cinerea strain t-459-V. The cross-species transmission was succeeded only by inoculation of mixed spores of L. biglobosa and B. cinerea on PDA or on stems of oilseed rape with the efficiency of 4.6% and 18.8%, respectively. To investigate viral cross-species transmission between L. biglobosa and B. cinerea in nature, RNA sequencing was carried out on L. biglobosa and B. cinerea isolates obtained from Brassica samples co-infected by these two pathogens and showed that at least two mycoviruses were detected in both fungal groups. These results indicate that cross-species transmission of mycoviruses may occur frequently in nature and result in the phenotypical changes of newly invaded phytopathogenic fungi. This study also provides new insights for using asymptomatic mycoviruses as biocontrol agent.
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Novel Mycoviruses Discovered from a Metatranscriptomics Survey of the Phytopathogenic Alternaria Fungus. Viruses 2022; 14:v14112552. [PMID: 36423161 PMCID: PMC9693364 DOI: 10.3390/v14112552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Alternaria fungus can cause notable diseases in cereals, ornamental plants, vegetables, and fruits around the world. To date, an increasing number of mycoviruses have been accurately and successfully identified in this fungus. In this study, we discovered mycoviruses from 78 strains in 6 species of the genus Alternaria, which were collected from 10 pear production areas using high-throughput sequencing technology. Using the total RNA-seq, we detected the RNA-dependent RNA polymerase of 19 potential viruses and the coat protein of two potential viruses. We successfully confirmed these viruses using reverse transcription polymerase chain reaction with RNA as the template. We identified 12 mycoviruses that were positive-sense single-stranded RNA (+ssRNA) viruses, 5 double-strand RNA (dsRNA) viruses, and 4 negative single-stranded RNA (-ssRNA) viruses. In these viruses, five +ssRNA and four -ssRNA viruses were novel mycoviruses classified into diverse the families Botourmiaviridae, Deltaflexivirus, Mymonaviridea, and Discoviridae. We identified a novel -ssRNA mycovirus isolated from an A. tenuissima strain HB-15 as Alternaria tenuissima negative-stranded RNA virus 2 (AtNSRV2). Additionally, we characterized a novel +ssRNA mycovirus isolated from an A. tenuissima strain SC-8 as Alternaria tenuissima deltaflexivirus 1 (AtDFV1). According to phylogenetic and sequence analyses, we determined that AtNSRV2 was related to the viruses of the genus Sclerotimonavirus in the family Mymonaviridae. We also found that AtDFV1 was related to the virus family Deltaflexivirus. This study is the first to use total RNA sequencing to characterize viruses in Alternaria spp. These results expand the number of Alternaria viruses and demonstrate the diversity of these mycoviruses.
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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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21
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Teng L, Chen S, Hu Z, Chen J, Liu H, Zhang T. Molecular characterization and transcriptomic analysis of a novel polymycovirus in the fungus Talaromyces amestolkiae. Front Microbiol 2022; 13:1008409. [PMID: 36386701 PMCID: PMC9645161 DOI: 10.3389/fmicb.2022.1008409] [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: 07/31/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022] Open
Abstract
Talaromyces amestolkiae is an important fungal species owing to its ubiquity in soils, plants, air, and food. In this study, we identified a novel six-segmented polymycovirus, Talaromyces amestolkiae polymycovirus 1 (TaPmV-1). Each of the double-stranded (ds) RNA segments of TaPmV-1 contained a single open reading frame, and the proteins encoded by dsRNA1, dsRNA2, dsRNA3, and dsRNA 5 shared significant amino acid identities of 56, 40, 47, and 43%, respectively, with the corresponding proteins of Aspergillus fumigatus polymycovirus-1(AfuPmV-1). DsRNA1, dsRNA3, and dsRNA5 of TaPmV-1 encoded an RNA-dependent RNA polymerase (RdRp), a viral methyltransferase, and a PAS-rich protein, respectively. The functions of the proteins encoded by dsRNA2, dsRNA4, and dsRNA6 have not been elucidated. Comparison of the virus-infected strain LSH3 with virus-cured strain LSHVF revealed that infection with TaPmV-l may reduce the production of red pigments and induce the clustering of fungal sclerotia. Furthermore, transcriptomic analyses demonstrated that infection with TaPmV-l downregulated the expression of transcripts related to metabolism, and may correlate with the reduced production of red pigments and clustering of sclerotia in T. amestolkiae. These results of this study provide novel insights into the mechanism of fungal gene regulation by polymycovirus infections at the transcriptome level, and this study is the first to report a novel polymycovirus of T. amestolkiae.
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Affiliation(s)
- Li Teng
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Sen Chen
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Zuquan Hu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Jili Chen
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Hongmei Liu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
- *Correspondence: Hongmei Liu, ; Tingting Zhang,
| | - Tingting Zhang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou, School of Basic Medical Science, Guizhou Medical University, Guiyang, China
- *Correspondence: Hongmei Liu, ; Tingting Zhang,
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22
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Shamsi W, Kondo H, Ulrich S, Rigling D, Prospero S. Novel RNA viruses from the native range of Hymenoscyphus fraxineus, the causal fungal agent of ash dieback. Virus Res 2022; 320:198901. [PMID: 36058013 DOI: 10.1016/j.virusres.2022.198901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022]
Abstract
The native Japanese population of the fungus Hymenoscyphus fraxineus, the causal agent of ash dieback in Europe, was screened for viruses using a high-throughput sequencing method. Five RNA viruses were detected in 116 fungal isolates sequenced via Illumina RNA-seq platform, with an overall virus prevalence of 11.2%. The viruses were completely sequenced by RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) followed by Sanger sequencing. The sequences appear to represent new species from three established families (Mito-, Endorna- and Partitiviridae), one recognized genus (Botybirnavirus) and a negative-sense single-stranded RNA virus in the order Bunyavirales from the proposed family "Mybuviridae". The highest prevalence was found for the mitovirus (7.8%), that had two genomic forms (linear and circular), while the other viruses were detected each in one isolate. Co-infection of a mitovirus and an endornavirus was also observed in one of the infected isolates. Here we describe the molecular characterization of the identified viruses. This study expands the diversity of viruses in H. fraxineus and provides the basis for investigating the virus-mediated control of ash dieback in Europe.
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Affiliation(s)
- Wajeeha Shamsi
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Sven Ulrich
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Daniel Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
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23
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Li Y, Liu S, Guo K, Ding W, Wang R. Virome of Pseudostellaria heterophylla: Identification and characterization of three novel carlaviruses and one novel amalgavirus associated with viral diseases of Pseudostellaria heterophylla. Front Microbiol 2022; 13:955089. [PMID: 36246219 PMCID: PMC9559581 DOI: 10.3389/fmicb.2022.955089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
Pseudostellaria heterophylla is a traditional Chinese herbal medicine, which has been cultivated for hundreds of years. Viral diseases of P. heterophylla occur widely and limit the yield and quality of this medicinal plant. In this study, five leaf samples of P. heterophylla with typical viral symptoms were collected from four main producing regions that are distributed in Fujian, Guizhou, and Anhui Provinces in China and analyzed by next-generation sequencing. Comprehensive bioinformatics analyses revealed that nine viruses in five genera Carlavirus, Potyvirus, Fabavirus, Cucumovirus, and Amalgavirus infected P. heterophylla. Among these viruses, three novel and two known carlaviruses, tentatively designated Pseudostellaria heterophylla carlavirus 1, 2, and 3 (PhCV1, PhCV2, and PhCV3), Jasmine virus C isolate Ph (Ph-JVC) and Stevia carlavirus 1 isolate Ph (Ph-StCV1), respectively, were first identified in P. heterophylla. PhCV1-3 share a similar genomic organization and clear sequence homology with members in the genus Carlavirus and could potentially be classified as new species of this genus. One novel amalgavirus, tentatively designated P. heterophylla amalgavirus 1 (PhAV1), was first identified in P. heterophylla. It had a typical genomic organization of the genus Amalgavirus. In PhAV1, the + 1 programmed ribosomal frameshifting, which is prevalent in most amalgaviruses, was identified and used in the expression of RNA-dependent RNA polymerase (RdRp). Combined with a phylogenetic analysis, PhAV1 could potentially be classified as new species of the genus Amalgavirus. In addition, multiple Broad bean wilt virus 2 (BBWV2) variants, Turnip mosaic virus (TuMV), and Cucumber mosaic virus (CMV), which have been reported in P. heterophylla, were also detected in this study. The distribution of PhCV1-3, Ph-JVC, Ph-StCV1, TuMV, BBWV2, and CMV in four production regions in Fujian, Guizhou, and Anhui Provinces was determined. This study increased our understanding of P. heterophylla virome and provided valuable information for the development of a molecular diagnostic technique and control of viral diseases in P. heterophylla.
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Kondo H, Botella L, Suzuki N. Mycovirus Diversity and Evolution Revealed/Inferred from Recent Studies. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:307-336. [PMID: 35609970 DOI: 10.1146/annurev-phyto-021621-122122] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High-throughput virome analyses with various fungi, from cultured or uncultured sources, have led to the discovery of diverse viruses with unique genome structures and even neo-lifestyles. Examples in the former category include splipalmiviruses and ambiviruses. Splipalmiviruses, related to yeast narnaviruses, have multiple positive-sense (+) single-stranded (ss) RNA genomic segments that separately encode the RNA-dependent RNA polymerase motifs, the hallmark of RNA viruses (members of the kingdom Orthornavirae). Ambiviruses appear to have an undivided ssRNA genome of 3∼5 kb with two large open reading frames (ORFs) separated by intergenic regions. Another narna-like virus group has two fully overlapping ORFs on both strands of a genomic segment that span more than 90% of the genome size. New virus lifestyles exhibited by mycoviruses include the yado-kari/yado-nushi nature characterized by the partnership between the (+)ssRNA yadokarivirus and an unrelated dsRNA virus (donor of the capsid for the former) and the hadaka nature of capsidless 10-11 segmented (+)ssRNA accessible by RNase in infected mycelial homogenates. Furthermore, dsRNA polymycoviruses with phylogenetic affinity to (+)ssRNA animal caliciviruses have been shown to be infectious as dsRNA-protein complexes or deproteinized naked dsRNA. Many previous phylogenetic gaps have been filled by recently discovered fungal and other viruses, which haveprovided interesting evolutionary insights. Phylogenetic analyses and the discovery of natural and experimental cross-kingdom infections suggest that horizontal virus transfer may have occurred and continue to occur between fungi and other kingdoms.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| | - Leticia Botella
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University, Brno, Czech Republic
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
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25
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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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De Miccolis Angelini RM, Raguseo C, Rotolo C, Gerin D, Faretra F, Pollastro S. The Mycovirome in a Worldwide Collection of the Brown Rot Fungus Monilinia fructicola. J Fungi (Basel) 2022; 8:jof8050481. [PMID: 35628739 PMCID: PMC9147972 DOI: 10.3390/jof8050481] [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: 03/20/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
The fungus Monilinia fructicola is responsible for brown rot on stone and pome fruit and causes heavy yield losses both pre- and post-harvest. Several mycoviruses are known to infect fungal plant pathogens. In this study, a metagenomic approach was applied to obtain a comprehensive characterization of the mycovirome in a worldwide collection of 58 M. fructicola strains. Deep sequencing of double-stranded (ds)RNA extracts revealed a great abundance and variety of mycoviruses. A total of 32 phylogenetically distinct positive-sense (+) single-stranded (ss)RNA viruses were identified. They included twelve mitoviruses, one in the proposed family Splipalmiviridae, and twelve botourmiaviruses (phylum Lenarviricota), eleven of which were novel viral species; two hypoviruses, three in the proposed family Fusariviridae, and one barnavirus (phylum Pisuviricota); as well as one novel beny-like virus (phylum Kitrinoviricota), the first one identified in Ascomycetes. A partial sequence of a new putative ssDNA mycovirus related to viruses within the Parvoviridae family was detected in a M. fructicola isolate from Serbia. The availability of genomic sequences of mycoviruses will serve as a solid basis for further research aimed at deepening the knowledge on virus–host and virus–virus interactions and to explore their potential as biocontrol agents against brown rot disease.
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Córdoba L, Ruiz-Padilla A, Rodríguez-Romero J, Ayllón MA. Construction and Characterization of a Botrytis Virus F Infectious Clone. J Fungi (Basel) 2022; 8:jof8050459. [PMID: 35628716 PMCID: PMC9146958 DOI: 10.3390/jof8050459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
Botrytis virus F (BVF) is a positive-sense, single-stranded RNA (+ssRNA) virus within the Gammaflexiviridae family of the plant-pathogenic fungus Botrytis cinerea. In this study, the complete sequence of a BVF strain isolated from B. cinerea collected from grapevine fields in Spain was analyzed. This virus, in this work BVF-V448, has a genome of 6827 nt in length, excluding the poly(A) tail, with two open reading frames encoding an RNA dependent RNA polymerase (RdRP) and a coat protein (CP). The 5′- and 3′-terminal regions of the genome were determined by rapid amplification of cDNA ends (RACE). Furthermore, a yet undetected subgenomic RNA species in BVF-V448 was identified, indicating that the CP is expressed via 3′ coterminal subgenomic RNAs (sgRNAs). We also report the successful construction of the first BVF full-length cDNA clone and synthesized in vitro RNA transcripts using the T7 polymerase, which could efficiently transfect two different strains of B. cinerea, B05.10 and Pi258.9. The levels of growth in culture and virulence on plants of BVF-V448 transfected strains were comparable to BVF-free strains. The infectious clones generated in this work provide a useful tool for the future development of an efficient BVF foreign gene expression vector and a virus-induced gene silencing (VIGS) vector as a biological agent for the control of B. cinerea.
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Affiliation(s)
- Laura Córdoba
- 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, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
| | - Ana Ruiz-Padilla
- 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, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
| | - Julio 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, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - María 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, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Correspondence:
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Genome Sequence of Sclerotinia sclerotiorum Hypovirulence-Associated DNA Virus 1 Found in the Fungus Penicillium olsonii Isolated from Washington State, USA. Microbiol Resour Announc 2022; 11:e0001922. [PMID: 35285691 PMCID: PMC9022559 DOI: 10.1128/mra.00019-22] [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] [Indexed: 11/20/2022] Open
Abstract
We report the discovery of a Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) isolate, named SsHADV1_PO, from the fungus Penicillium olsonii isolated from Washington state, USA. The genome of SsHADV1_PO is 2,166 bp and contains two open reading frames, with more than 98% nucleotide identity with respect to reported SsHADV-1 isolates.
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Luo X, Jiang D, Xie J, Jia J, Duan J, Cheng J, Fu Y, Chen T, Yu X, Li B, Lin Y. Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum. Viruses 2022; 14:v14030456. [PMID: 35336865 PMCID: PMC8953294 DOI: 10.3390/v14030456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Endornaviruses are capsidless linear (+) ssRNA viruses in the family Endornaviridae. In this study, Scelrotinia sclerotiorum endornavirus 11 (SsEV11), a novel endornavirus infecting hypovirulent Sclerotinia sclerotiorum strain XY79, was identified and cloned using virome sequencing analysis and rapid amplification of cDNA ends (RACE) techniques. The full-length genome of SsEV11 is 11906 nt in length with a large ORF, which encodes a large polyprotein of 3928 amino acid residues, containing a viral methyltransferase domain, a cysteine-rich region, a putative DEADc, a viral helicase domain, and an RNA-dependent RNA polymerase (RdRp) 2 domain. The 5’ and 3’ untranslated regions (UTR) are 31 nt and 90 nt, respectively. According to the BLAST result of the nucleotide sequence, SsEV11 shows the highest identity (45%) with Sclerotinia minor endornavirus 1 (SmEV1). Phylogenetic analysis based on amino acid sequence of RdRp demonstrated that SsEV11 clusters to endornavirus and has a close relationship with Betaendornavirus. Phylogenetic analysis based on the sequence of endornaviral RdRp domain indicated that there were three large clusters in the phylogenetic tree. Combining the results of alignment analysis, Cluster I at least has five subclusters including typical members of Alphaendornavirus and many unclassified endornaviruses that isolated from fungi, oomycetes, algae, and insects; Cluster II also has five subclusters including typical members of Betaendornavirus, SsEV11, and other unclassified viruses that infected fungi; Cluster III includes many endorna-like viruses that infect nematodes, mites, and insects. Viruses in Cluster I and Cluster II are close to each other and relatively distant to those in Cluster III. Our study characterized a novel betaendornavirus, SsEV11, infected fungal pathogen S. sclerotiorum, and suggested that notable phylogenetic diverse exists in endornaviruses. In addition, at least, one novel genus, Gammaendornavirus, should be established to accommodate those endorna-like viruses in Cluster III.
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Affiliation(s)
- Xin Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
| | - 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.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - 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.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - 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.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Xiao Yu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Bo Li
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - 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.); (J.C.); (Y.F.); (X.Y.); (B.L.)
- Correspondence:
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Zhu W, Yang J, Lu S, Jin D, Pu J, Wu S, Luo XL, Liu L, Li Z, Xu J. RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China. Front Microbiol 2022; 13:780651. [PMID: 35250920 PMCID: PMC8894885 DOI: 10.3389/fmicb.2022.780651] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Most emerging and re-emerging viruses causing infectious diseases in humans and domestic animals have originated from wildlife. However, current knowledge of the spectrum of RNA viruses in the Qinghai-Tibet Plateau in China is still limited. Here, we performed metatranscriptomic sequencing on fecal samples from 56 birds and 91 small mammals in Tibet and Qinghai Provinces, China, to delineate their viromes and focused on vertebrate RNA viruses. A total of 184 nearly complete genome RNA viruses belonging to 28 families were identified. Among these, 173 new viruses shared <90% amino acid identity with previously known viral sequences. Several of these viruses, such as those belonging to genera Orthonairovirus and Hepatovirus, could be zoonotic viruses. In addition, host taxonomy and geographical location of these viruses showed new hosts and distribution of several previously discovered viruses. Moreover, 12 invertebrate RNA viruses were identified with <40% amino acid identity to known viruses, indicating that they belong to potentially new taxa. The detection and characterization of RNA viruses from wildlife will broaden our knowledge of virus biodiversity and possible viral diseases in the Qinghai–Tibet Plateau.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Research Institute of Public Heath, Nankai University, Tianjin, China
- *Correspondence: Jianguo Xu,
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Characterization of a Novel Mycovirus from the Phytopathogenic Fungus Botryosphaeria dothidea. Viruses 2022; 14:v14020331. [PMID: 35215923 PMCID: PMC8879742 DOI: 10.3390/v14020331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/10/2022] Open
Abstract
Botryosphaeria dothidea is, globally, one of the most economically important phytopathogenic fungi worldwide, causing the canker and dieback of fruit trees. An increasing number of viruses infecting B. dothidea have lately been reported, several of which could confer hypovirulence. In this study, isolated from strain ZM170285-1 of B. dothidea, a novel double-stranded RNA (dsRNA) mycovirus, tentatively named Botryosphaeria dothidea partitivirus 2 (BdPV2), was identified well. The BdPV2 harbored three dsRNA segments (1–3) with lengths of 1751, 1568, and 1198 bp, which encoded an RNA-dependent RNA polymerase (RdRp), a capsid protein (CP), and a hypothetical protein of unknown function, respectively. BLASTp searches revealed that the predicted protein sequences of dsRNA1 and dsRNA2 had the highest identities (74.95% and 61.01%) with the corresponding dsRNAs of Penicillium stoloniferum virus S (PsV-S), whereas dsRNA3 shared the highest identity (32.95%) with the dsRNA3 of Aspergillus ochraceous virus 1 (AoV1). Phylogenetic analysis indicated that BdPV2 belonged to the Gammapartitivirus genus and Partitiviridae family. To our knowledge, this is the first report of a gammapartitivirus in B. dothidea.
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Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li S, Li L, Lǐ J, Liu H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa A, Paraskevopoulou S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya T, Schulze AD, Schwemmle M, Shi M, Shí X, Shí Z, Shimomoto Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada A, Takeuchi S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka Y, Tomonaga K, Tordo N, Torto B, Towner JS, Tsuda S, Tu C, Turina M, Tzanetakis IE, Uchida J, Usugi T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang LF, Wang G, Wang Y, Wang Y, Waqas M, Wèi T, Wen S, Whitfield AE, Williams JV, Wolf YI, Wu J, Xu L, Yanagisawa H, Yang C, Yang Z, Zerbini FM, Zhai L, Zhang YZ, Zhang S, Zhang J, Zhang Z, Zhou X. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3513-3566. [PMID: 34463877 PMCID: PMC8627462 DOI: 10.1007/s00705-021-05143-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R Agwanda
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture & Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, Davis, CA, USA
| | - Carol D Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Republic of South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuya Chiaki
- Grape and Persimmon Research Station, Institute of Fruit tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W Ferguson
- School of Veterinary Medicine, St. George's University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin, Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD, USA
| | - Tong Han
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London, UK
| | - Jiang Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - John S Hu
- University of Hawaii, Honolulu, HI, USA
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - M Ilyas
- Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Gilda B Jonson
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research, Berlin, Germany
| | - Fujio Kadono
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Kenji Kubota
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Longhui Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service , Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liege, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | - Michael Melzer
- Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Tobi J Ming
- Molecular Genetics, Pacific Biological Station, Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J Mordecai
- Department of Medicine, Univeristy of British Columbia, Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Adam C Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A Patterson
- Fisheries and Oceans Canada, Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz, Rio de Janeiro, Brazil
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Angela D Schulze
- Molecular Genetics Lab, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shigeharu Takeuchi
- Japan Plant Protection Association Kochi Experiment Station, Konan, Kochi, Japan
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Amy Teffer
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Yasuhiro Tomitaka
- Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, Japan
| | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), , Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Shinya Tsuda
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People's Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System,, Fayetteville, AR, 72701, USA
| | | | - Tomio Usugi
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People's Republic of China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiangxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Caixia Yang
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei , People's Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, People's Republic of China
| | - Zhe Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Porter AF, Cobbin J, Li CX, Eden JS, Holmes EC. Metagenomic Identification of Viral Sequences in Laboratory Reagents. Viruses 2021; 13:v13112122. [PMID: 34834931 PMCID: PMC8625350 DOI: 10.3390/v13112122] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/16/2022] Open
Abstract
Metagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterise the complete 'infectome' (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing ("metatranscriptomics") we documented the presence of contaminant viral sequences in multiple 'blank' negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication-associated protein encoding (CRESS) DNA virus-like sequences were recovered in the blank control libraries, as well as contaminating sequences from the Totiviridae, Tombusviridae and Lentiviridae families of RNA virus. These data suggest that viral contamination of common laboratory reagents is likely commonplace and can comprise a wide variety of viruses.
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Affiliation(s)
- Ashleigh F. Porter
- The Peter Doherty Institute of Immunity and Infection, Department of Microbiology and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Joanna Cobbin
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (J.-S.E.)
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ci-Xiu Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, China;
| | - John-Sebastian Eden
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (J.-S.E.)
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (J.-S.E.)
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Correspondence:
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Characterization of the Mycovirome from the Plant-Pathogenic Fungus Cercospora beticola. Viruses 2021; 13:v13101915. [PMID: 34696345 PMCID: PMC8537984 DOI: 10.3390/v13101915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 12/25/2022] Open
Abstract
Cercospora leaf spot (CLS) caused by Cercospora beticola is a devastating foliar disease of sugar beet (Beta vulgaris), resulting in high yield losses worldwide. Mycoviruses are widespread fungi viruses and can be used as a potential biocontrol agent for fugal disease management. To determine the presence of mycoviruses in C. beticola, high-throughput sequencing analysis was used to determine the diversity of mycoviruses in 139 C. beticola isolates collected from major sugar beet production areas in China. The high-throughput sequencing reads were assembled and searched against the NCBI database using BLASTn and BLASTx. The results showed that the obtained 93 contigs were derived from eight novel mycoviruses, which were grouped into 3 distinct lineages, belonging to the families Hypoviridae, Narnaviridae and Botourmiaviridae, as well as some unclassified (−)ssRNA viruses in the order Bunyavirales and Mononegavirales. To the best of our knowledge, this is the first identification of highly diverse mycoviruses in C. beticola. The novel mycoviruses explored in this study will provide new viral materials to biocontrol Cercospora diseases. Future studies of these mycoviruses will aim to assess the roles of each mycovirus in biological function of C. beticola in the future.
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Mu F, Li B, Cheng S, Jia J, Jiang D, Fu Y, Cheng J, Lin Y, Chen T, Xie J. Nine viruses from eight lineages exhibiting new evolutionary modes that co-infect a hypovirulent phytopathogenic fungus. PLoS Pathog 2021; 17:e1009823. [PMID: 34428260 PMCID: PMC8415603 DOI: 10.1371/journal.ppat.1009823] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/03/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Mycoviruses are an important component of the virosphere, but our current knowledge of their genome organization diversity and evolution remains rudimentary. In this study, the mycovirus composition in a hypovirulent strain of Sclerotinia sclerotiorum was molecularly characterized. Nine mycoviruses were identified and assigned into eight potential families. Of them, six were close relatives of known mycoviruses, while the other three had unique genome organizations and evolutionary positions. A deltaflexivirus with a tripartite genome has evolved via arrangement and horizontal gene transfer events, which could be an evolutionary connection from unsegmented to segmented RNA viruses. Two mycoviruses had acquired a second helicase gene by two different evolutionary mechanisms. A rhabdovirus representing an independent viral evolutionary branch was the first to be confirmed to occur naturally in fungi. The major hypovirulence-associated factor, an endornavirus, was finally corroborated. Our study expands the diversity of mycoviruses and potential virocontrol agents, and also provides new insights into virus evolutionary modes including virus genome segmentation. Identification of mycoviruses in phytopathogenic fungi is necessary for understanding the origin of viruses and developing virocontrol strategies to protect plants. Nine mycoviruses with RNA genomes were identified in a hypovirulent strain of Sclerotinia sclerotiorum and were classified into eight potential viral families, suggesting that the composition of mycoviral communities was complex in this single fungal strain. They included four previously characterized mycoviruses and three distant relatives of known mycoviruses, as well as the first reports of a deltaflexivirus with a tripartite genome, and a fungal rhabdovirus. In addition, we found an endornavirus associated with hypovirulence in a phytopathogenic fungus. Our study makes a significant contribution because it not only expands the diversity-related knowledge of mycoviruses and potential virocontrol agents, but also provides new insights into mycovirus evolution.
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Affiliation(s)
- Fan Mu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shufen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- 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 Hongshan Laboratory, 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
| | - 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
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Abstract
The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal- and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update of the Genomoviridae, a number of new members of this family have been sequenced. Here, we report on the most recent taxonomic update, including the creation of one new genus, Gemytripvirus, and classification of ~420 new genomoviruses into 164 new species. We also announce the adoption of the "Genus + freeform epithet" binomial system for the naming of all 236 officially recognized species in the family Genomoviridae. The updated taxonomy presented in this article has been accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France.
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Mu F, Jia J, Xue Y, Jiang D, Fu Y, Cheng J, Lin Y, Xie J. Characterization of a novel botoulivirus isolated from the phytopathogenic fungus Sclerotinia sclerotiorum. Arch Virol 2021; 166:2859-2863. [PMID: 34291341 DOI: 10.1007/s00705-021-05168-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/22/2021] [Indexed: 10/20/2022]
Abstract
Sclerotinia sclerotiorum ourmiavirus 17 (SsOV17) was isolated from the hypovirulent strain GF3 of Sclerotinia sclerotiorum. The genome of SsOV17 is 2,802 nt in length and contains a single long open reading frame (ORF) flanked by a short structured 5'-untranslated region (5'-UTR) (28 nt) and a long 3'-UTR (788 nt), respectively. The ORF encodes a protein with 663 amino acids and a predicted molecular mass of 75.0 kDa. A BLASTp search indicated that the protein encoded by SsOV17 is closely related to the putative RNA-dependent RNA polymerase (RdRp) of Sclerotinia sclerotiorum ourmiavirus 13 (71% identity). A multiple sequence alignment indicated that eight conserved amino acid motifs were present in the RdRp conserved region of SsOV17. Phylogenetic analysis demonstrated that SsOV17 clustered with members of the genus Botoulivirus.
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Affiliation(s)
- Fan Mu
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunxiang Xue
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanping Fu
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang Lin
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, 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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Abstract
Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named "ambiviruses" with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains.
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Jia J, Fu Y, Jiang D, Mu F, Cheng J, Lin Y, Li B, Marzano SYL, Xie J. Interannual dynamics, diversity and evolution of the virome in Sclerotinia sclerotiorum from a single crop field. Virus Evol 2021; 7:veab032. [PMID: 33927888 PMCID: PMC8058396 DOI: 10.1093/ve/veab032] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mycovirus diversity is generally analyzed from isolates of fungal culture isolates at a single point in time as a snapshot. The stability of mycovirus composition within the same geographical location over time remains unclear. Not knowing how the population fluctuates in the field can be a source of unpredictability in the successful application of virocontrol. To better understand the changes over time, we monitored the interannual dynamics and abundance of mycoviruses infecting Sclerotinia sclerotiorum at a rapeseed-growing field for three years. We found that the virome in S. sclerotiorum harbors unique mycovirus compositions each year. In total, sixty-eight mycoviruses were identified, among which twenty-four were detected in all three successive years. These twenty-four mycoviruses can be classified as the members of the core virome in this S. sclerotiorum population, which show persistence and relatively high transmissibility under field conditions. Nearly two-thirds of the mycoviruses have positive-sense, single-stranded RNA genomes and were found consistently across all three years. Moreover, twenty-eight mycoviruses are newly described, including four novel, multi-segmented narnaviruses, and four unique bunyaviruses. Overall, the newly discovered mycoviruses in this study belong to as many as twenty families, into which eight were first identified in S. sclerotiorum, demonstrating evolutionarily diverse viromes. Our findings not only shed light on the annual variation of mycovirus diversity but also provide important virus evolutionary clues.
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Affiliation(s)
- Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
| | - Fan Mu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
| | - Shin-Yi Lee Marzano
- United States Department of Agriculture/Agricultural Research Service, Toledo, OH 43606, USA
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan 430070, People's Republic of China
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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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Chen F, Pu Z, Ni H, Wang Y, Yan B. Multiple mycoviruses identified in Pestalotiopsis spp. from Chinese bayberry. Virol J 2021; 18:43. [PMID: 33622359 PMCID: PMC7903649 DOI: 10.1186/s12985-021-01513-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 12/02/2022] Open
Abstract
Background Chinese bayberry (Myrica rubra) is a subtropical fruit crop widely grown in southern China. Twig dieback is a disease of Chinese bayberry caused by Pestalotiopsis spp. and results in great economic losses to Chinese bayberry production. A virus survey was conducted in the population of Pestalotiopsis spp. infecting M. rubra in China. We explored the viral diversity in Pestalotiopsis spp., which may provide resources for further development as biocontrol agents of twig dieback. Methods Strains of Pestalotiopsis spp. were isolated from diseased twigs of M. rubra, and cultured on potato dextrose agar for RNA extraction. The total RNA of each strain was extracted, mixed, and used for RNA sequencing. The resulting sequences were deduplicated, annotated, and then used for phylogenetic analysis. Results Seven novel viruses were characterized from 59 isolates of M. rubra collected from 14 localities in China. Based on the phylogenetic analysis, these viruses were classified into five viral families/orders, Botourmiaviridae, Mitoviridae, Partitiviridae, Tymovirales and Bunyavirales, and one virus, Pestalotiopsis negative-stranded RNA virus 1, which likely belongs to a new viral family. Conclusions Metatranscriptomics analysis showed the presence of various mycoviruses in Pestalotiopsis spp. isolated from M. rubra in China. The genomes of eight putative viruses were identified, seven of which were nearly full-length. Some of these viruses of Pestalotiopsis spp. may have the potential for the biological control of twig dieback of M. rubra. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01513-3.
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Affiliation(s)
- Fangyong Chen
- Citrus Research Institute of Zhejiang Province, Taizhou, 318026, China.
| | - Zhanxu Pu
- Citrus Research Institute of Zhejiang Province, Taizhou, 318026, China
| | - Haizhi Ni
- Citrus Research Institute of Zhejiang Province, Taizhou, 318026, China
| | - Yin Wang
- Citrus Research Institute of Zhejiang Province, Taizhou, 318026, China
| | - Bangguo Yan
- Citrus Research Institute of Zhejiang Province, Taizhou, 318026, China
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Filippou C, Diss RM, Daudu JO, Coutts RHA, Kotta-Loizou I. The Polymycovirus-Mediated Growth Enhancement of the Entomopathogenic Fungus Beauveria bassiana Is Dependent on Carbon and Nitrogen Metabolism. Front Microbiol 2021; 12:606366. [PMID: 33603722 PMCID: PMC7884332 DOI: 10.3389/fmicb.2021.606366] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Polymycoviridae is a growing family of mycoviruses whose members typically have non-conventional capsids and multi-segmented, double-stranded (ds) RNA genomes. Beauveria bassiana polymycovirus (BbPmV) 1 is known to enhance the growth and virulence of its fungal host, the entomopathogenic ascomycete and popular biological control agent B. bassiana. Here we report the complete sequence of BbPmV-3, which has six genomic dsRNA segments. Phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) protein sequences revealed that BbPmV-3 is closely related to the partially sequenced BbPmV-2 but not BbPmV-1. Nevertheless, both BbPmV-3 and BbPmV-1 have similar effects on their respective host isolates ATHUM 4946 and EABb 92/11-Dm, affecting pigmentation, sporulation, and radial growth. Production of conidia and radial growth are significantly enhanced in virus-infected isolates as compared to virus-free isogenic lines on Czapek-Dox complete and minimal media that contain sucrose and sodium nitrate. However, this polymycovirus-mediated effect on growth is dependent on the carbon and nitrogen sources available to the host fungus. Both BbPmV-3 and BbPmV-1 increase growth of ATHUM 4946 and EABb 92/11-Dm when sucrose is replaced by lactose, trehalose, glucose, or glycerol, while the effect is reversed on maltose and fructose. Similarly, both BbPmV-3 and BbPmV-1 decrease growth of ATHUM 4946 and EABb 92/11-Dm when sodium nitrate is replaced by sodium nitrite, potassium nitrate, or ammonium nitrate. In conclusion, the effects of polymycoviruses on B. bassiana are at least partially mediated via its metabolic pathways.
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Affiliation(s)
- Charalampos Filippou
- Department of Life Sciences, Imperial College London, London, United Kingdom.,Department of Clinical, Pharmaceutical and Biological Science, University of Hertfordshire, Hatfield, United Kingdom
| | - Rebecca M Diss
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - John O Daudu
- Department of Clinical, Pharmaceutical and Biological Science, University of Hertfordshire, Hatfield, United Kingdom
| | - Robert H A Coutts
- Department of Clinical, Pharmaceutical and Biological Science, University of Hertfordshire, Hatfield, United Kingdom
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College London, London, United Kingdom
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Wang J, Ni Y, Liu X, Zhao H, Xiao Y, Xiao X, Li S, Liu H. Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents. Virus Evol 2020; 7:veaa095. [PMID: 33505706 PMCID: PMC7816680 DOI: 10.1093/ve/veaa095] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Macrophomina phaseolina is an important necrotrophic phytopathogenic fungus and cause extensive damage in many oilseed crops. Twelve M.phaseolina isolates with diverse biological phenotypes were selected for a high-throughput sequencing-based metatranscriptomic and bioinformatics analysis to identify viruses infecting M.phaseolina. The analysis identified 40 partial or nearly complete viral genome segments, 31 of which were novel viruses. Among these viral sequences, 43% of the viral genomes were double-stranded RNA (dsRNA), 47% were positive single-stranded RNA (ssRNA+), and the remaining 10% were negative sense-stranded RNA (ssRNA−). The 40 viruses showed affinity to 13 distinct viral lineages, including Bunyavirales (four viruses), Totiviridae (three viruses), Chrysoviridae (five viruses), Partitiviridae (four viruses), Hypoviridae (one virus), Endornaviridae (two viruses), Tombusviridae (three viruses), Narnaviridae (one virus), Potyviridae (one virus), Bromoviridae (one virus), Virgaviridae (six viruses), ‘Fusagraviridae’ (five viruses), and Ourmiavirus (four viruses). Two viruses are closely related to two families, Potyviridae and Bromoviridae, which previously contained no mycovirus species. Moreover, nine novel viruses associated with M.phaseolina were identified in the family Totiviridae, Endornaviridae, and Partitiviridae. Coinfection with multiple viruses is prevalent in M.phaseolina, with each isolate harboring different numbers of viruses, ranging from three to eighteen. Furthermore, the effects of the viruses on the fungal host were analyzed according to the biological characteristics of each isolate. The results suggested that M.phaseolina hypovirus 2, M.phaseolina fusagravirus virus 1-5 (MpFV1-5), M.phaseolina endornavirus 1-2 (MpEV1-2), M.phaseolina ourmia-like virus 1-3 (MpOLV1-3), M.phaseolina mitovirus 4 (MpMV4), and M.phaseolina mycobunyavirus 1-4 (MpMBV1-4) were only detected in hypovirulent isolates. Those viruses associated with hypovirulence might be used as biological control agents as an environmentally friendly alternative to chemical fungicides. These findings considerably expand our understanding of mycoviruses in M.phaseolina and unvailed the presence of a huge difference among viruses in isolates from different hosts in distant geographical regions. Together, the present study provides new knowledge about viral evolution and fungus-virus coevolution.
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Affiliation(s)
- Jing Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China.,Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Yannong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province, PR China
| | - Xueqiong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province, PR China
| | - Shujun Li
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
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Mycoviral diversity and characteristics of a negative-stranded RNA virus LeNSRV1 in the edible mushroom Lentinula edodes. Virology 2020; 555:89-101. [PMID: 33308828 DOI: 10.1016/j.virol.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/04/2020] [Accepted: 11/12/2020] [Indexed: 11/23/2022]
Abstract
Bioinformatics and RT-PCR analysis of RNA from four Lentinula edodes samples identified 22 different virus-like contigs comprising 15 novel and 3 previously reported viruses. We further investigated the Lentinula edodes negative-stranded RNA virus 1 (LeNSRV1) isolated from a symptomatic sample, whose virion is a filamentous particle with a diameter of ~15 nm and a length of ~1200 nm. RT-PCR analysis detected LeNSRV1 in 10 of the 56 Chinese L. edodes core collection strains and 6 of the 22 monokaryotic strains from the L. edodes strain HNZMD. Genetic variation analysis showed that the sequences encoding the nucleocapsid protein (ORF2) from all the aforementioned LeNSRV1 positive strains are very conservative. The results presented here may enrich our understanding of L. edodes virus diversity and the characteristics of LeNSRV1, and will promote further research on virus-host interaction in L. edodes.
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Honda S, Eusebio-Cope A, Miyashita S, Yokoyama A, Aulia A, Shahi S, Kondo H, Suzuki N. Establishment of Neurospora crassa as a model organism for fungal virology. Nat Commun 2020; 11:5627. [PMID: 33159072 PMCID: PMC7648066 DOI: 10.1038/s41467-020-19355-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungus Neurospora crassa is used as a model organism for genetics, developmental biology and molecular biology. Remarkably, it is not known to host or to be susceptible to infection with any viruses. Here, we identify diverse RNA viruses in N. crassa and other Neurospora species, and show that N. crassa supports the replication of these viruses as well as some viruses from other fungi. Several encapsidated double-stranded RNA viruses and capsid-less positive-sense single-stranded RNA viruses can be experimentally introduced into N. crassa protoplasts or spheroplasts. This allowed us to examine viral replication and RNAi-mediated antiviral responses in this organism. We show that viral infection upregulates the transcription of RNAi components, and that Dicer proteins (DCL-1, DCL-2) and an Argonaute (QDE-2) participate in suppression of viral replication. Our study thus establishes N. crassa as a model system for the study of host-virus interactions. The fungus Neurospora crassa is a model organism for the study of various biological processes, but it is not known to be infected by any viruses. Here, Honda et al. identify RNA viruses that infect N. crassa and examine viral replication and RNAi-mediated antiviral responses, thus establishing this fungus as a model for the study of host-virus interactions.
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Affiliation(s)
- Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Ana Eusebio-Cope
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza- Aoba, Sendai, 980-0845, Japan
| | - Ayumi Yokoyama
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Annisa Aulia
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan.
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47
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Jo Y, Back CG, Choi H, Cho WK. Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics. PLANTS 2020; 9:plants9081052. [PMID: 32824817 PMCID: PMC7464454 DOI: 10.3390/plants9081052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/16/2020] [Indexed: 11/16/2022]
Abstract
The dried peach fruits clinging to peach trees or lying on the ground nearby are known as mummified peach fruits. Here, we examined the microbiome communities of three different mummified peach fruits from the nectarine cultivar "Hahong" by DNA- and RNA-sequencing. We found the dominance of Monilinia fructigena followed by Sclerotinia borealis, S. sclerotiorum, and Botrytis cinerea in the mummified peach fruits. Moreover, we found a high number of Proteobacteria, including Frateuria aurantia, Neoasaia chiangmaiensis, Robbsia andropogonis, and Ewingella Americana. Furthermore, we identified several viruses and viroids. Bacteriophages were identified by DNA- and RNA-sequencing, while viruses and viroids with RNA genomes were identified by only RNA-sequencing. Moreover, we identified a novel mycovirus referred to as Monilinia umbra-like virus 1 (MULV1) from M. fructigena. Our results revealed the co-inhabitance of fungi and bacteria in the mummified peach fruits, although dominant microorganisms were present. RNA-sequencing revealed that several fungal and bacterial genes were actively transcribed. Comparative analyses suggested that RNA-sequencing provides more detailed information on microbial communities; however, combining DNA- and RNA-sequencing results increased the diversity of microorganisms, suggesting the importance of databases and analysis tools for microbiome studies. Taken together, our study provides a comprehensive overview of microbial communities in mummified peach fruits by DNA shotgun sequencing and RNA-sequencing.
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Affiliation(s)
- Yeonhwa Jo
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (H.C.)
| | - Chang-Gi Back
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 55365, Korea;
| | - Hoseong Choi
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (H.C.)
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (H.C.)
- Correspondence: ; Tel.: +82-2-880-4687
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48
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Yang M, Zhou X, Zhai L, Xiao F, Hong N, Wang G. Molecular characterization of a novel mycovirus infecting the phytopathogenic fungus Botryosphaeria dothidea. Arch Virol 2020; 165:1667-1670. [PMID: 32328855 DOI: 10.1007/s00705-020-04629-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022]
Abstract
In this study, we report the molecular characterization of a novel positive-sense single-stranded RNA (+ssRNA) mycovirus from Botryosphaeria dothidea strain G91, which we name "Botryosphaeria dothidea botourmiavirus 1" (BdBOV-1). The complete genome of BdBOV-1 is 2547 nucleotides (nt) long, contains one open reading frame (ORF) potentially encoding an RNA-dependent RNA polymerase (RdRp), and shows a close relationship to mycoviruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp sequences confirmed that BdBOV-1 clustered together with the members of the family Botourmiaviridae. To the best of our knowledge, this is the first report of a +ssRNA mycovirus infecting B. dothidea.
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Affiliation(s)
- Mengmeng Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, People's Republic of China
| | - Xiaoqi Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Lifeng Zhai
- College of Life Science and Technology, Yangtze Normal University, Chongqing, 408000, People's Republic of China
| | - Feng Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, People's Republic of China.
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49
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Telengech P, Hisano S, Mugambi C, Hyodo K, Arjona-López JM, López-Herrera CJ, Kanematsu S, Kondo H, Suzuki N. Diverse Partitiviruses From the Phytopathogenic Fungus, Rosellinia necatrix. Front Microbiol 2020; 11:1064. [PMID: 32670213 PMCID: PMC7332551 DOI: 10.3389/fmicb.2020.01064] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/29/2020] [Indexed: 01/18/2023] Open
Abstract
Partitiviruses (dsRNA viruses, family Partitiviridae) are ubiquitously detected in plants and fungi. Although previous surveys suggested their omnipresence in the white root rot fungus, Rosellinia necatrix, only a few of them have been molecularly and biologically characterized thus far. We report the characterization of a total of 20 partitiviruses from 16 R. necatrix strains belonging to 15 new species, for which “Rosellinia necatrix partitivirus 11–Rosellinia necatrix partitivirus 25” were proposed, and 5 previously reported species. The newly identified partitiviruses have been taxonomically placed in two genera, Alphapartitivirus, and Betapartitivirus. Some partitiviruses were transfected into reference strains of the natural host, R. necatrix, and an experimental host, Cryphonectria parasitica, using purified virions. A comparative analysis of resultant transfectants revealed interesting differences and similarities between the RNA accumulation and symptom induction patterns of R. necatrix and C. parasitica. Other interesting findings include the identification of a probable reassortment event and a quintuple partitivirus infection of a single fungal strain. These combined results provide a foundation for further studies aimed at elucidating mechanisms that underly the differences observed.
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Affiliation(s)
- Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Cyrus Mugambi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Juan Manuel Arjona-López
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.,Institute for Sustainable Agriculture, Spanish Research Council, Córdoba, Spain
| | | | - Satoko Kanematsu
- Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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50
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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.
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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
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