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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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Lu X, Dai Z, Xue J, Li W, Ni P, Xu J, Zhou C, Zhang W. Discovery of novel RNA viruses through analysis of fungi-associated next-generation sequencing data. BMC Genomics 2024; 25:517. [PMID: 38797853 PMCID: PMC11129472 DOI: 10.1186/s12864-024-10432-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Like all other species, fungi are susceptible to infection by viruses. The diversity of fungal viruses has been rapidly expanding in recent years due to the availability of advanced sequencing technologies. However, compared to other virome studies, the research on fungi-associated viruses remains limited. RESULTS In this study, we downloaded and analyzed over 200 public datasets from approximately 40 different Bioprojects to explore potential fungal-associated viral dark matter. A total of 12 novel viral sequences were identified, all of which are RNA viruses, with lengths ranging from 1,769 to 9,516 nucleotides. The amino acid sequence identity of all these viruses with any known virus is below 70%. Through phylogenetic analysis, these RNA viruses were classified into different orders or families, such as Mitoviridae, Benyviridae, Botourmiaviridae, Deltaflexiviridae, Mymonaviridae, Bunyavirales, and Partitiviridae. It is possible that these sequences represent new taxa at the level of family, genus, or species. Furthermore, a co-evolution analysis indicated that the evolutionary history of these viruses within their groups is largely driven by cross-species transmission events. CONCLUSIONS These findings are of significant importance for understanding the diversity, evolution, and relationships between genome structure and function of fungal viruses. However, further investigation is needed to study their interactions.
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Affiliation(s)
- Xiang Lu
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Ziyuan Dai
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People's Hospital, Yancheng, Jiangsu, China
| | - Jiaxin Xue
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Ping Ni
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Juan Xu
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Wen Zhang
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China.
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, 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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4
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Shi N, Zhu Q, Yang G, Wang P, Huang B. Prevalence and species diversity of dsRNA mycoviruses from Beauveria bassiana strains in the China's Guniujiang nature. Heliyon 2024; 10:e30186. [PMID: 38694113 PMCID: PMC11061733 DOI: 10.1016/j.heliyon.2024.e30186] [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: 09/09/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
We investigated the prevalence and species diversity of dsRNA mycoviruses in Beauveria bassiana isolates from the China's Guniujiang Nature Preserve. Among the 28 isolates analyzed, electropherotyping revealed viral infections in 28.6 % (8 out of 28) of the isolates. Metatranscriptomic identification and RT-PCR confirmed the presence of six putative virus species, including two novel species: Beauveria bassiana victorivirus 2 (BbV-2) and Beauveria bassiana bipartite mycovirus 2 (BbBV-2). Four previously characterized mycoviruses were also identified: Beauveria bassiana polymycovirus 4 (BbPmV4), Beauveria bassiana partitivirus 1 (BbPV-1), Beauveria bassiana bipartite mycovirus 1 (BbBV-1), and Beauveria bassiana chrysovirus 2 (BbCV-2). BbPmV4 was found to be the prevailing mycovirus among the infected isolates, and three isolates showed co-infection with both BbPmV4 and BbBV-2. This study enhances our understanding of fungal viral taxonomy and diversity, providing insights into mycovirus infections in B. bassiana populations in China's Guniujiang Nature Preserve. Furthermore, the study on the diversity of B. bassiana viruses lays the foundation for recognizing fungal viruses as potential enhancers of biocontrol agents.
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Affiliation(s)
- Najie Shi
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Qiuyan Zhu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Guogen Yang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Ping Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
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Zhou K, Zhang F, Deng Y. Comparative Analysis of Viromes Identified in Multiple Macrofungi. Viruses 2024; 16:597. [PMID: 38675938 PMCID: PMC11054281 DOI: 10.3390/v16040597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Macrofungi play important roles in the soil elemental cycle of terrestrial ecosystems. Fungal viruses are common in filamentous fungi, and some of them can affect the growth and development of hosts. However, the composition and evolution of macrofungal viruses are understudied. In this study, ninety strains of Trametes versicolor, Coprinellus micaceus, Amanita strobiliformis, and Trametes hirsuta were collected in China. Four mixed pools were generated by combining equal quantities of total RNA from each strain, according to the fungal species, and then subjected to RNA sequencing. The sequences were assembled, annotated, and then used for phylogenetic analysis. Twenty novel viruses or viral fragments were characterized from the four species of macrofungi. Based on the phylogenetic analysis, most of the viral contigs were classified into ten viral families or orders: Barnaviridae, Benyviridae, Botourmiaviridae, Deltaflexiviridae, Fusariviridae, Hypoviridae, Totiviridae, Mitoviridae, Mymonaviridae, and Bunyavirales. Of these, ambi-like viruses with circular genomes were widely distributed among the studied species. Furthermore, the number and overall abundance of viruses in these four species of macrofungi (Basidiomycota) were found to be much lower than those in broad-host phytopathogenic fungi (Ascomycota: Sclerotinia sclerotiorum, and Botrytis cinerea). By employing metatranscriptomic analysis in this study, for the first time, we demonstrated the presence of multiple mycoviruses in Amanita strobiliformis, Coprinellus micaceus, Trametes hirsute, and Trametes versicolor, significantly contributing to research on mycoviruses in macrofungi.
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Affiliation(s)
- Kang Zhou
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang 236037, China
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang 236037, China
| | - Fan Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Deng
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu 610066, 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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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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8
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Zhang Z, Guo W, Lu Y, Kang Q, Sui L, Liu H, Zhao Y, Zou X, Li Q. Hypovirulence-associated mycovirus epidemics cause pathogenicity degeneration of Beauveria bassiana in the field. Virol J 2023; 20:255. [PMID: 37924080 PMCID: PMC10623766 DOI: 10.1186/s12985-023-02217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The entomogenous fungus Beauveria bassiana is used as a biological insecticide worldwide, wild B. bassiana strains with high pathogenicity in the field play an important role in controlling insect pests via not only screening of highly virulent strains but also natural infection, but the pathogenicity degeneration of wild strains severely affected aforementioned effects. Previous studies have showed that multiple factors contributed to this phenomenon. It has been extensively proved that the mycovirus infection caused hypovirulence of phytopathogenic fungi, which has been used for plant disease biocontrol. However, it remains unknown whether the mycovirus epidemics is a key factor causing hypovirulence of B. bassiana naturally in the field. METHODS Wild strains of B. bassiana were collected from different geographic locations in Jilin Province, China, to clarify the epidemic and diversity of the mycoviruses. A mycovirus Beauveria bassiana chrysovirus 2 (BbCV2) we have previously identified was employed to clarify its impact on the pathogenicity of host fungi B. bassiana against the larvae of insect pest Ostrinia furnacalis. The serological analysis was conducted by preparing polyclonal antibody against a BbCV2 coat protein, to determine whether it can dissociate outside the host fungal cells and subsequently infect new hosts. Transcriptome analysis was used to reveal the interactions between viruses and hosts. RESULTS We surprisingly found that the mycovirus BbCV2 was prevalent in the field as a core virus in wild B. bassiana strains, without obvious genetic differentiation, this virus possessed efficient and stable horizontal and vertical transmission capabilities. The serological results showed that the virus could not only replicate within but also dissociate outside the host cells, and the purified virions could infect B. bassiana by co-incubation. The virus infection causes B. bassiana hypovirulence. Transcriptome analysis revealed decreased expression of genes related to insect epidermis penetration, hypha growth and toxin metabolism in B. bassiana caused by mycovirus infection. CONCLUSION Beauveria bassiana infected by hypovirulence-associated mycovirus can spread the virus to new host strains after infecting insects, and cause the virus epidemics in the field. The findings confirmed that mycovirus infection may be an important factor affecting the pathogenicity degradation of B. bassiana in the field.
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Affiliation(s)
- Zhengkun Zhang
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Wenbo Guo
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Yang Lu
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Qin Kang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 101408, People's Republic of China
| | - Li Sui
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Hongyu Liu
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Yu Zhao
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Xiaowei Zou
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China
| | - Qiyun Li
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, People's Republic of China.
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, People's Republic of China.
- Jilin Agricultural Science and Technology University, Jilin, 132109, People's Republic of China.
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Pedersen C, Marzano SYL. Mechanisms of Primed Defense: Plant Immunity Induced by Endophytic Colonization of a Mycovirus-Induced Hypovirulent Fungal Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:726-736. [PMID: 37459471 DOI: 10.1094/mpmi-06-23-0083-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
How mycovirus-induced hypovirulence in fungi activates plant defense is still poorly understood. The changes in plant fitness and gene expression caused by the inoculation of the fungus Sclerotinia sclerotiorum harboring and made hypovirulent by the mycovirus soybean leaf-associated gemygorvirus-1 (SlaGemV-1) of the species Gemycircularvirus soybe1 were examined in this study. As the hypovirulent fungus (DK3V) colonized soybean Glycine max, plant transcriptomic analysis indicated changes in defense responses and photosynthetic activity, supported by an upregulation of individual genes and overrepresentation of photosystem gene ontology groups. The upregulated genes include genes relating to both pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity as well as various genes relating to the induction of systemic acquired resistance and the biosynthesis of jasmonic acid. Plants colonized with DK3V showed a resistant phenotype to virulent S. sclerotiorum infection. Plant height and leaf area were also determined to be larger in plants grown with the virus-infected fungus. Here, we hypothesize that inoculation of soybean with DK3V can result in the triggering of a wide range of defense mechanisms to prime against later infection. The knowledge gained from this study about plant transcriptomics and phenotype will help prime plant immunity with mycovirus-infected hypovirulent fungal strains more effectively. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Connor Pedersen
- United States Department of Agriculture-Agricultural Research Service, Toledo, OH 43606, U.S.A
| | - Shin-Yi Lee Marzano
- United States Department of Agriculture-Agricultural Research Service, Toledo, OH 43606, U.S.A
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Wen Y, Qu J, Zhang H, Yang Y, Huang R, Deng J, Zhang J, Xiao Y, Li J, Zhang M, Wang G, Zhai L. Identification and Characterization of a Novel Hypovirus from the Phytopathogenic Fungus Botryosphaeria dothidea. Viruses 2023; 15:2059. [PMID: 37896836 PMCID: PMC10611357 DOI: 10.3390/v15102059] [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: 08/22/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Many mycoviruses have been accurately and successfully identified in plant pathogenic fungus Botryosphaeria dothidea. This study discovered three mycoviruses from a B. dothidea strain SXD111 using high-throughput sequencing technology. A novel hypovirus was tentatively named Botryosphaeria dothidea hypovirus 1 (BdHV1/SXD111). The other two were known viruses, which we named Botryosphaeria dothidea polymycovirus 1 strain SXD111 (BdPmV1/SXD111) and Botryosphaeria dothidea partitivirus 1 strain SXD111 (BdPV1/SXD111). The genome of BdHV1/SXD111 is 11,128 nucleotides long, excluding the poly (A) tail. A papain-like cysteine protease (Pro), a UDP-glucose/sterol glucosyltransferase (UGT), an RNA-dependent RNA polyprotein (RdRp), and a helicase (Hel) were detected in the polyprotein of BdHV1/SXD111. Phylogenetic analysis showed that BdHV1/SXD111 was clustered with betahypovirus and separated from members of the other genera in the family Hypoviridae. The BdPmV1/SXD111 genome comprised five dsRNA segments with 2396, 2232, 1967, 1131, and 1060 bp lengths. Additionally, BdPV1/SXD111 harbored three dsRNA segments with 1823, 1623, and 557 bp lengths. Furthermore, the smallest dsRNA was a novel satellite component of BdPV1/SXD111. BdHV1/SXD111 could be transmitted through conidia and hyphae contact, whereas it likely has no apparent impact on the morphologies and virulence of the host fungus. Thus, this study is the first report of a betahypovirus isolated from the fungus B. dothidea. Importantly, our results significantly enhance the diversity of the B. dothidea viruses.
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Affiliation(s)
- Yongqi Wen
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jinyue Qu
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Honglin Zhang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Yi Yang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Rui Huang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jili Deng
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jiayu Zhang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Yanping Xiao
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jiali Li
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Meixin Zhang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Lifeng Zhai
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
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11
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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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12
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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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13
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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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14
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Li W, Sun H, Cao S, Zhang A, Zhang H, Shu Y, Chen H. Extreme Diversity of Mycoviruses Present in Single Strains of Rhizoctonia cerealis, the Pathogen of Wheat Sharp Eyespot. Microbiol Spectr 2023; 11:e0052223. [PMID: 37436153 PMCID: PMC10433806 DOI: 10.1128/spectrum.00522-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/18/2023] [Indexed: 07/13/2023] Open
Abstract
Rhizoctonia cerealis is the pathogen of wheat sharp eyespot, which occurs throughout temperate wheat-growing regions of the world. In this project, the genomes of viruses from four strains of R. cerealis were analyzed based on Illumina high-throughput transcriptome sequencing (RNA-Seq) data. After filtering out reads that mapped to the fungal genome, viral genomes were assembled. In total, 131 virus-like sequences containing complete open reading frames (ORFs), belonging to 117 viruses, were obtained. Based on phylogenetic analysis, some of them were identified as novel members of the families Curvulaviridae, Endornaviridae, Hypoviridae, Mitoviridae, Mymonaviridae, and Phenuiviridae, while others were unclassified viruses. Most of these viruses from R. cerealis were significantly different from the viruses already reported. We propose the establishment of a new family, Rhizoctobunyaviridae, and two new genera, Rhizoctobunyavirus and Iotahypovirus. We further clarified the distribution and coinfection of these viruses in the four strains. Surprisingly, 39 viral genomes of up to 12 genera were found in strain R1084. Strain R0942, containing the fewest viruses, also contained 21 viral genomes belonging to 10 genera. Based on the RNA-Seq data, we estimated the accumulation level of some viruses in host cells and found that the mitoviruses in R. cerealis generally have very high accumulation. In conclusion, in the culturable phytopathogenic fungus R. cerealis, we discovered a considerable diversity of mycoviruses and a series of novel viruses. This study expands our understanding of the mycoviral diversity in R. cerealis and provides a rich resource for the further use of mycoviruses to control wheat sharp eyespot. IMPORTANCE Rhizoctonia cerealis is a binucleate fungus that is widely distributed worldwide and can cause sharp eyespot disease in cereal crops. In this study, 131 virus-like sequences belonging to 117 viruses were obtained based on analysis of high-throughput RNA-Seq data from four strains of R. cerealis. Many of these viruses were novel members of various virus families, while others were unclassified viruses. As a result, a new family named Rhizoctobunyaviridae and two new genera, Rhizoctobunyavirus and Iotahypovirus, were proposed. Moreover, the discovery of multiple viruses coinfecting a single host and the high accumulation levels of mitoviruses have shed light on the complex interactions between different viruses in a single host. In conclusion, a significant diversity of mycoviruses was discovered in the culturable phytopathogenic fungus R. cerealis. This study expands our understanding of mycoviral diversity, and provides a valuable resource for the further utilization of mycoviruses to control wheat diseases.
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Affiliation(s)
- Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Haiyan Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Aixiang Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Haotian Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Yan Shu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
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15
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Jia J, Chen X, Wang X, Liu X, Zhang N, Zhang B, Chang Y, Mu F. Molecular characterization of a novel ambiguivirus isolated from the phytopathogenic fungus Setosphaeria turcica. Arch Virol 2023; 168:199. [PMID: 37400663 DOI: 10.1007/s00705-023-05829-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/05/2023] [Indexed: 07/05/2023]
Abstract
In this study, a novel single-stranded RNA virus was isolated from the plant-pathogenic fungus Setosphaeria turcica strain TG2, and the virus was named "Setosphaeria turcica ambiguivirus 2" (StAV2). The complete nucleotide sequence of the StAV2 genome was determined using RT-PCR and RLM-RACE. The StAV2 genome comprises 3,000 nucleotides with a G+C content of 57.77%. StAV2 contains two in-frame open reading frames (ORFs) with the potential to produce an ORF1-ORF2 fusion protein via a stop codon readthrough mechanism. ORF1 encodes a hypothetical protein (HP) of unknown function. The ORF2-encoded protein shows a high degree of sequence similarity to the RNA-dependent RNA polymerases (RdRps) of ambiguiviruses. BLASTp searches showed that the StAV2 HP and RdRp share the highest amino acid sequence identity (46.38% and 69.23%, respectively) with the corresponding proteins of a virus identified as "Riboviria sp." isolated from a soil sample. Multiple sequence alignments and phylogenetic analysis based on the amino acid sequences of the RdRp revealed that StAV2 is a new member of the proposed family "Ambiguiviridae".
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Affiliation(s)
- Jichun Jia
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xu Chen
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xue Wang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xu Liu
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Nuo Zhang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Baojun Zhang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yindong Chang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Fan Mu
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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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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18
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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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19
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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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20
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Characterization of a Fungal Virus Representing a Novel Genus in the Family Alphaflexiviridae. Viruses 2023; 15:v15020339. [PMID: 36851552 PMCID: PMC9967154 DOI: 10.3390/v15020339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Sclerotinia sclerotiorum is an ascomycetous fungus and hosts various mycoviruses. In this study, a novel fungal alphaflexivirus with a special genomic structure, named Sclerotinia sclerotiorum alphaflexivirus 1 (SsAFV1), was cloned from a hypovirulent strain, AHS31. Strain AHS31 was also co-infected with two botourmiaviruses and two mitoviruses. The complete genome of SsAFV1 comprised 6939 bases with four open reading frames (ORFs), a conserved 5'-untranslated region (UTR), and a poly(A) tail in the 3' terminal; the ORF1 and ORF3 encoded a replicase and a coat protein (CP), respectively, while the function of the proteins encoded by ORF2 and ORF4 was unknown. The virion of SsAFV1 was flexuous filamentous 480-510 nm in length and 9-10 nm in diameter. The results of the alignment and the phylogenetic analysis showed that SsAFV1 is related to allexivirus and botrexvirus, such as Garlic virus X of the genus Allexivirus and Botrytis virus X of the genus Botrevirus, both with 44% amino-acid (aa) identity of replicase. Thus, SsAFV1 is a novel virus and a new genus, Sclerotexvirus, is proposed to accommodate this novel alphaflexivirus.
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21
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Chiba Y, Yabuki A, Takaki Y, Nunoura T, Urayama SI, Hagiwara D. The First Identification of a Narnavirus in Bigyra, a Marine Protist. Microbes Environ 2023; 38. [PMID: 36858534 PMCID: PMC10037099 DOI: 10.1264/jsme2.me22077] [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] [Indexed: 03/03/2023] Open
Abstract
Current information on the diversity and evolution of eukaryotic RNA viruses is biased towards host lineages, such as animals, plants, and fungi. Although protists represent the majority of eukaryotic diversity, our understanding of the protist RNA virosphere is still limited. To reveal untapped RNA viral diversity, we screened RNA viruses from 30 marine protist isolates and identified a novel RNA virus named Haloplacidia narnavirus 1 (HpNV1). A phylogenetic ana-lysis revealed that HpNV1 is a new member of the family Narnaviridae. The present study filled a gap in the distribution of narnaviruses and implies their wide distribution in Stramenopiles.
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Affiliation(s)
- Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
| | - Akinori Yabuki
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba
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22
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Ayllón MA, Vainio EJ. Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle. Adv Virus Res 2023; 115:1-86. [PMID: 37173063 DOI: 10.1016/bs.aivir.2023.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.
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Affiliation(s)
- María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain; Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
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23
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Kuhn JH, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bandte M, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Bigarré L, Blair CD, Blasdell KR, Bradfute SB, Briese T, Brown PA, Bruggmann R, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Candresse T, Carson J, Casas I, Chandran K, Charrel RN, Chiaki Y, Crane A, Crane M, Dacheux L, Bó ED, de la Torre JC, de Lamballerie X, de Souza WM, de Swart RL, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Feuvrier C, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, García ML, García-Sastre A, Garrison AR, Godwin SE, Gonzalez JPJ, de Bellocq JG, Griffiths A, Groschup MH, Günther S, Hammond J, Hepojoki J, Hierweger MM, Hongō S, Horie M, Horikawa H, Hughes HR, Hume AJ, Hyndman TH, Jiāng D, Jonson GB, Junglen S, Kadono F, Karlin DG, Klempa B, Klingström J, Koch MC, Kondō H, Koonin EV, Krásová J, Krupovic M, Kubota K, Kuzmin IV, Laenen L, Lambert AJ, Lǐ J, Li JM, Lieffrig F, Lukashevich IS, Luo D, Maes P, Marklewitz M, Marshall SH, Marzano SYL, McCauley JW, Mirazimi A, Mohr PG, Moody NJG, Morita Y, Morrison RN, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Neriya Y, Netesov SV, Neumann G, Nowotny N, Ochoa-Corona FM, Palacios G, Pallandre L, Pallás V, Papa A, Paraskevopoulou S, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Pérez DR, Pfaff F, Plemper RK, Postler TS, Pozet F, Radoshitzky SR, Ramos-González PL, Rehanek M, Resende RO, Reyes CA, Romanowski V, Rubbenstroth D, Rubino L, Rumbou A, Runstadler JA, Rupp M, Sabanadzovic S, Sasaya T, Schmidt-Posthaus H, Schwemmle M, Seuberlich T, Sharpe SR, Shi M, Sironi M, Smither S, Song JW, Spann KM, Spengler JR, Stenglein MD, Takada A, Tesh RB, Těšíková J, Thornburg NJ, Tischler ND, Tomitaka Y, Tomonaga K, Tordo N, Tsunekawa K, Turina M, Tzanetakis IE, Vaira AM, van den Hoogen B, Vanmechelen B, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Whitfield AE, Williams JV, Wolf YI, Yamasaki J, Yanagisawa H, Ye G, Zhang YZ, Økland AL. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2022; 167:2857-2906. [PMID: 36437428 PMCID: PMC9847503 DOI: 10.1007/s00705-022-05546-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In March 2022, 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 two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. 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 (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - 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
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - 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
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Greifswald, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, Starkville, MS, USA
| | - Martina Bandte
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Éric Bergeron
- Division of High-Consequence Pathogens and Pathology, Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nadine Biedenkopf
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Laurent Bigarré
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - 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
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Paul A Brown
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - 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, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- 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
| | | | | | - Jeremy Carson
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - 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
| | - Yuya Chiaki
- Division of Fruit Tree and Tea Pest Control Research, Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Mark Crane
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | - Laurent Dacheux
- Institut Pasteur, Université Paris Cité, Unit Lyssavirus Epidemiology and Neuropathology, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Paris, France
| | - 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
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Rik L de Swart
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 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
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Toufic Elbeaino
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Koray Ergünay
- Department of Medical Microbiology, Virology Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC, USA
| | - Guozhong Feng
- China National Rice Research Institute, Hangzhou, China
| | | | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Scott E Godwin
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, USA
| | | | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Melanie M Hierweger
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Seiji Hongō
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | | | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Adam J Hume
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Gilda B Jonson
- International Rice Research Institute, College, Los Baños, 4032, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fujio Kadono
- Clinical Plant Science Center, Hosei University, Tokyo, Japan
| | - David G Karlin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Michel C Koch
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - 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
| | - Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Kenji Kubota
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Ivan V Kuzmin
- The University of Texas Medical Branch at Galveston, Galveston, TX, 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
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jun-Min Li
- Institute of Plant Virology, Ningbo University, Ningbo, 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
| | - Dongsheng Luo
- Institut Pasteur, Université Paris Cité, Unit Lyssavirus Epidemiology and Neuropathology, Paris, France
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Sergio H Marshall
- Instituto de Biología-Laboratorio de Genética Molecular-Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service, Toledo, OH, USA
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Peter G Mohr
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | - Nick J G Moody
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | | | - Richard N Morrison
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - 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
| | | | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Yutaro Neriya
- School of Agriculture, Utsunomiya University, Utsunomiya, Japan
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, 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
| | - Francisco M Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics. Stillwater, Oklahoma State University, Oklahoma, USA
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurane Pallandre
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidat Politècnica de Valencia, Valencia, Spain
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - 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
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | | | - Richard K Plemper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, USA
| | | | - Marius Rehanek
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Unversidad Nacional de La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Unversidad Nacional de La Plata, Buenos Aires, Argentina
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Artemis Rumbou
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease & Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Melanie Rupp
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Heike Schmidt-Posthaus
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Torsten Seuberlich
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stephen R Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, China
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - 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 M 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, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Nicole D Tischler
- Laboratorio de Virología Molecular, Centro Ciencia & Vida, Fundación Ciencia & Vida and Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Yasuhiro Tomitaka
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Keizō Tomonaga
- Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur de Guinée, BP 4416, Conakry, Guinea
| | | | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Nikos Vasilakis
- The University of Texas Medical Branch at Galveston, 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
| | - 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
| | - Junki Yamasaki
- Environmental Agriculture Promotion Division, Department of Agricultural Development, Kochi Prefectural Government, Kochi, Kochi, Japan
| | | | - Gongyin Ye
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China
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Discovery, Genomic Sequence Characterization and Phylogenetic Analysis of Novel RNA Viruses in the Turfgrass Pathogenic Colletotrichum spp. in Japan. Viruses 2022; 14:v14112572. [PMID: 36423181 PMCID: PMC9698584 DOI: 10.3390/v14112572] [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: 09/20/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Turfgrass used in various areas of the golf course has been found to present anthracnose disease, which is caused by Colletotrichum spp. To obtain potential biological agents, we identified four novel RNA viruses and obtained full-length viral genomes from turfgrass pathogenic Colletotrichum spp. in Japan. We characterized two novel dsRNA partitiviruses: Colletotrichum associated partitivirus 1 (CaPV1) and Colletotrichum associated partitivirus 2 (CaPV2), as well as two negative single-stranded (ss) RNA viruses: Colletotrichum associated negative-stranded RNA virus 1 (CaNSRV1) and Colletotrichum associated negative-stranded RNA virus 2 (CaNSRV2). Using specific RT-PCR assays, we confirmed the presence of CaPV1, CaPV2 and CaNSRV1 in dsRNAs from original and sub-isolates of Colletotrichum sp. MBCT-264, as well as CaNSRV2 in dsRNAs from original and sub-isolates of Colletotrichum sp. MBCT-288. This is the first time mycoviruses have been discovered in turfgrass pathogenic Colletotrichum spp. in Japan. CaPV1 and CaPV2 are new members of the newly proposed genus "Zetapartitivirus" and genus Alphapartitivirus, respectively, in the family Partitiviridae, according to genomic characterization and phylogenetic analysis. Negative sense ssRNA viruses CaNSRV1 and CaNSRV2, on the other hand, are new members of the family Phenuiviridae and the proposed family "Mycoaspirividae", respectively. These findings reveal previously unknown RNA virus diversity and evolution in turfgrass pathogenic Colletotrichum spp.
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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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Rodriguez Coy L, Plummer KM, Khalifa ME, MacDiarmid RM. Mycovirus-encoded suppressors of RNA silencing: Possible allies or enemies in the use of RNAi to control fungal disease in crops. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:965781. [PMID: 37746227 PMCID: PMC10512228 DOI: 10.3389/ffunb.2022.965781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/21/2022] [Indexed: 09/26/2023]
Abstract
Plants, fungi, and many other eukaryotes have evolved an RNA interference (RNAi) mechanism that is key for regulating gene expression and the control of pathogens. RNAi inhibits gene expression, in a sequence-specific manner, by recognizing and deploying cognate double-stranded RNA (dsRNA) either from endogenous sources (e.g. pre-micro RNAs) or exogenous origin (e.g. viruses, dsRNA, or small interfering RNAs, siRNAs). Recent studies have demonstrated that fungal pathogens can transfer siRNAs into plant cells to suppress host immunity and aid infection, in a mechanism termed cross-kingdom RNAi. New technologies, based on RNAi are being developed for crop protection against insect pests, viruses, and more recently against fungal pathogens. One example, is host-induced gene silencing (HIGS), which is a mechanism whereby transgenic plants are modified to produce siRNAs or dsRNAs targeting key transcripts of plants, or their pathogens or pests. An alternative gene regulation strategy that also co-opts the silencing machinery is spray-induced gene silencing (SIGS), in which dsRNAs or single-stranded RNAs (ssRNAs) are applied to target genes within a pathogen or pest. Fungi also use their RNA silencing machinery against mycoviruses (fungal viruses) and mycoviruses can deploy virus-encoded suppressors of RNAi (myco-VSRs) as a counter-defence. We propose that myco-VSRs may impact new dsRNA-based management methods, resulting in unintended outcomes, including suppression of management by HIGS or SIGS. Despite a large diversity of mycoviruses being discovered using high throughput sequencing, their biology is poorly understood. In particular, the prevalence of mycoviruses and the cellular effect of their encoded VSRs are under-appreciated when considering the deployment of HIGS and SIGS strategies. This review focuses on mycoviruses, their VSR activities in fungi, and the implications for control of pathogenic fungi using RNAi.
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Affiliation(s)
- Lorena Rodriguez Coy
- Australian Research Council Research Hub for Sustainable Crop Protection, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim M. Plummer
- Australian Research Council Research Hub for Sustainable Crop Protection, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Mahmoud E. Khalifa
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Robin M. MacDiarmid
- BioProtection, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Three-Layered Complex Interactions among Capsidless (+)ssRNA Yadokariviruses, dsRNA Viruses, and a Fungus. mBio 2022; 13:e0168522. [PMID: 36040032 PMCID: PMC9600902 DOI: 10.1128/mbio.01685-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have previously discovered a virus neo-lifestyle exhibited by a capsidless positive-sense (+), single-stranded (ss) RNA virus YkV1 (family Yadokariviridae) and an unrelated double-stranded (ds) RNA virus YnV1 (proposed family "Yadonushiviridae") in a phytopathogenic ascomycete, Rosellinia necatrix. YkV1 has been proposed to replicate in the capsid provided by YnV1 as if it were a dsRNA virus and enhance YnV1 replication in return. Recently, viruses related to YkV1 (yadokariviruses) have been isolated from diverse ascomycetous fungi. However, it remains obscure whether such viruses generally show the YkV1-like lifestyle. Here, we identified partner viruses for three distinct yadokariviruses, YkV3, YkV4a, and YkV4b, isolated from R. necatrix that were coinfected with multiple dsRNA viruses phylogenetically distantly related to YnV1. We first established transformants of R. necatrix carrying single yadokarivirus cDNAs and fused them with infectants by single partner candidate dsRNA viruses. Consequently, YkV3 and YkV4s replicated only in the presence of RnMBV3 (family Megabirnaviridae) and RnMTV1 (proposed family "Megatotiviridae"), respectively. The partners were mutually interchangeable between the two YkV4 strains and three RnMTV1 strains but not between other combinations involving YkV1 or YkV3. In contrast to YkV1 enhancing YnV1 accumulation, YkV4s reduced RnMTV1 accumulation to different degrees according to strains. Interestingly, YkV4 rescued the host R. necatrix from impaired growth induced by RnMTV1. YkV3 exerted no apparent effect on its partner (RnMBV3) or host fungus. Overall, we revealed that while yadokariviruses generally require partner dsRNA viruses for replication, each yadokarivirus partners with a different dsRNA virus species in the three diverse families and shows a distinct symbiotic relation in a fungus. IMPORTANCE A capsidless (+)ssRNA virus YkV1 (family Yadokariviridae) highjacks the capsid of an unrelated dsRNA virus YnV1 (proposed family "Yadonushiviridae") in a phytopathogenic ascomycete, while YkV1 trans-enhances YnV1 replication. Herein, we identified the dsRNA virus partners of three yadokariviruses (YkV3, YkV4a, and YkV4b) with genome organization different from YkV1 as being different from YnV1 at the suborder level. Their partners were mutually interchangeable between the two YkV4 strains and three strains of the partner virus RnMTV1 (proposed family "Megatotiviridae") but not between other combinations involving YkV1 or YkV3. Unlike YkV1, YkV4s reduced RnMTV1 accumulation and rescued the host fungus from impaired growth induced by RnMTV1. YkV3 exerted no apparent effect on its partner (RnMBV3, family Megabirnaviridae) or host fungus. These revealed that while each yadokarivirus has a species-specific partnership with a dsRNA virus, yadokariviruses collectively partner extremely diverse dsRNA viruses and show three-layered complex mutualistic/antagonistic interactions in a fungus.
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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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Galán-Cubero R, Córdoba L, Rodríguez-Romero J, Chiapello M, Turina M, Ayllón MA. Molecular Data of a Novel Penoulivirus Associated with the Plant-Pathogenic Fungus Erysiphe necator. PHYTOPATHOLOGY 2022; 112:1587-1591. [PMID: 35509205 DOI: 10.1094/phyto-12-21-0536-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Rocío Galán-Cubero
- 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 28223, Spain
| | - Laura Córdoba
- 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 28223, Spain
| | - Julio Rodríguez-Romero
- 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 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28040, Spain
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - 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 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28040, Spain
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Mycoviromic Analysis Unveils Complex Virus Composition in a Hypovirulent Strain of Sclerotinia sclerotiorum. J Fungi (Basel) 2022; 8:jof8070649. [PMID: 35887405 PMCID: PMC9317179 DOI: 10.3390/jof8070649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Mycoviruses are ubiquitous in pathogenic fungi including Sclerotinia sclerotiorum. Using RNA sequencing, more mycoviruses have been identified in individual strains, which were previously reported to be infected by a single mycovirus. A hypovirulent strain of S. sclerotiorum, HC025, was previously thought to harbor a single mitovirus, Sclerotinia sclerotiorum mitovirus 1 (SsMV1), based on the analysis of the conventional dsRNA extraction method. We found HC025 to be co-infected by five mycoviruses. In addition to SsMV1, four mycoviruses were identified: Sclerotinia sclerotiorum narnavirus 4 (SsNV4), Sclerotinia sclerotiorum negative-stranded RNA virus 1 (SsNSRV1), Sclerotinia sclerotiorum ourmia-like virus 14 (SsOLV14), and SsOLV22. Three mycoviruses including SsNV4, SsNSRV1, and SsOLV14 share high replicase identities (more than 95%) with the previously reported corresponding mycoviruses, and SsOLV22 shows lower identity to the known viruses. The complete genome of SsOLV22 is 3987 nt long and contains a single ORF-encoded RdRp, which shares 24.84% identity with the RNA-dependent RNA polymerase (RdRp) of Hubei narna-like virus 10 (query coverage: 26%; e-value: 8 × 10−19). The phylogenetic tree of RdRp suggests that SsOLV22 is a new member within the family Botourmiaviridae. All of the mycoviruses except for SsNSRV1 could horizontally co-transfer from HC025 to the virulent strain Ep-1PNA367 with hypovirulent phenotypes, and converted a later strain into a hypovirulent strain. In summary, we molecularly characterized the hypovirulent strain HC025 and identified five RNA mycoviruses including a new member within Botourmiaviridae.
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Raco M, Vainio EJ, Sutela S, Eichmeier A, Hakalová E, Jung T, Botella L. High Diversity of Novel Viruses in the Tree Pathogen Phytophthora castaneae Revealed by High-Throughput Sequencing of Total and Small RNA. Front Microbiol 2022; 13:911474. [PMID: 35783401 PMCID: PMC9244493 DOI: 10.3389/fmicb.2022.911474] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022] Open
Abstract
Phytophthora castaneae, an oomycete pathogen causing root and trunk rot of different tree species in Asia, was shown to harbor a rich diversity of novel viruses from different families. Four P. castaneae isolates collected from Chamaecyparis hodginsii in a semi-natural montane forest site in Vietnam were investigated for viral presence by traditional and next-generation sequencing (NGS) techniques, i.e., double-stranded RNA (dsRNA) extraction and high-throughput sequencing (HTS) of small RNAs (sRNAs) and total RNA. Genome organization, sequence similarity, and phylogenetic analyses indicated that the viruses were related to members of the order Bunyavirales and families Endornaviridae, Megabirnaviridae, Narnaviridae, Totiviridae, and the proposed family “Fusagraviridae.” The study describes six novel viruses: Phytophthora castaneae RNA virus 1–5 (PcaRV1-5) and Phytophthora castaneae negative-stranded RNA virus 1 (PcaNSRV1). All six viruses were detected by sRNA sequencing, which demonstrates an active RNA interference (RNAi) system targeting viruses in P. castaneae. To our knowledge, this is the first report of viruses in P. castaneae and the whole Phytophthora major Clade 5, as well as of the activity of an RNAi mechanism targeting viral genomes among Clade 5 species. PcaRV1 is the first megabirnavirus described in oomycetes and the genus Phytophthora.
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Affiliation(s)
- Milica Raco
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
- *Correspondence: Milica Raco,
| | - Eeva J. Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Suvi Sutela
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Aleš Eichmeier
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Brno, Czechia
| | - Eliška Hakalová
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Brno, Czechia
| | - Thomas Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
| | - Leticia Botella
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
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Zhang Y, Gao J, Li Y. Diversity of mycoviruses in edible fungi. Virus Genes 2022; 58:377-391. [PMID: 35668282 DOI: 10.1007/s11262-022-01908-6] [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: 01/17/2022] [Accepted: 04/21/2022] [Indexed: 11/25/2022]
Abstract
Mycoviruses (fungal viruses) are widespread in all major taxonomic groups of fungi. Although most mycovirus infections are latent, some mycoviruses, such as La France isometric virus, mushroom virus X, and oyster mushroom spherical virus, can cause severe diseases in edible fungi and lead to significant production losses. Recently, deep sequencing has been employed as a powerful research tool to identify new mycoviruses and to enhance our understanding of virus diversity and evolution. An increasing number of novel mycoviruses that can infect edible fungi have been reported, including double-stranded (ds) RNA, positive-sense ( +)ssRNA, and negative-sense (-)ssRNA viruses. To date, approximately 60 mycoviruses have been reported in edible fungi. In this review, we summarize the recent advances in the diversity and evolution of mycoviruses that can infect edible fungi. We also discuss mycovirus transmission, co-infections, and genetic variations, as well as the methods used to detect and control of mycoviruses in edible fungi, and provide insights for future research on mushroom viral diseases.
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Affiliation(s)
- Yanjing Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin, China
- Laboratory of Plant Pathology, College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Jie Gao
- Laboratory of Plant Pathology, College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin, China.
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Jiang Y, Yang B, Liu X, Tian X, Wang Q, Wang B, Zhang Q, Yu W, Qi X, Jiang Y, Hsiang T. A Satellite dsRNA Attenuates the Induction of Helper Virus-Mediated Symptoms in Aspergillus flavus. Front Microbiol 2022; 13:895844. [PMID: 35711767 PMCID: PMC9195127 DOI: 10.3389/fmicb.2022.895844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Aspergillus flavus is an important fungal pathogen of animals and plants. Previously, we reported a novel partitivirus, Aspergillus flavus partitivirus 1 (AfPV1), infecting A. flavus. In this study, we obtained a small double-stranded (ds) RNA segment (734 bp), which is a satellite RNA of the helper virus, AfPV1. The presence of AfPV1 altered the colony morphology, decreased the number of conidiophores, created significantly larger vacuoles, and caused more sensitivity to osmotic, oxidative, and UV stresses in A. flavus, but the small RNA segment could attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus. Moreover, AfPV1 infection reduced the pathogenicity of A. flavus in corn (Zea mays), honeycomb moth (Galleria mellonella), mice (Mus musculus), and the adhesion of conidia to host epithelial cells, and increased conidial death by macrophages. However, the small RNA segment could also attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus, perhaps by reducing the genomic accumulation of the helper virus AfPV1 in A. flavus. We used this model to investigate transcriptional genes regulated by AfPV1 and the small RNA segment in A. flavus, and their role in generating different phenotypes. We found that the pathways of the genes regulated by AfPV1 in its host were similar to those of retroviral viruses. Therefore, some pathways may be of benefit to non-retroviral viral integration or endogenization into the genomes of its host. Moreover, some potential antiviral substances were also found in A. flavus using this system.
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Affiliation(s)
- Yinhui Jiang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Yang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiang Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xun Tian
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qifang Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Yanping Jiang
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
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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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Abstract
RNA viruses usually have linear genomes and are encapsidated by their own capsids. Here, we newly identified four mycoviruses and two previously reported mycoviruses (a fungal reovirus and a botybirnavirus) in the hypovirulent strain SCH941 of Sclerotinia sclerotiorum. One of the newly discovered mycoviruses, Sclerotinia sclerotiorum yadokarivirus 1 (SsYkV1), with a nonsegmented positive-sense single-stranded RNA (+ssRNA) genome, was molecularly characterized. SsYkV1 is 5,256 nucleotides (nt) in length, excluding the poly(A) structure, and has a large open reading frame that putatively encodes a polyprotein with the RNA-dependent RNA polymerase (RdRp) domain and a 2A-like motif. SsYkV1 was phylogenetically positioned into the family Yadokariviridae and was most closely related to Rosellinia necatrix yadokarivirus 2 (RnYkV2), with 40.55% identity (78% coverage). Although SsYkV1 does not encode its own capsid protein, the RNA and RdRp of SsYkV1 are trans-encapsidated in virions of Sclerotinia sclerotiorum botybirnavirus 3 (SsBV3), a bisegmented double-stranded RNA (dsRNA) mycovirus within the genus Botybirnavirus. In this way, SsYkV1 likely replicates inside the heterocapsid comprised of the SsBV3 capsid protein, like a dsRNA virus. SsYkV1 has a limited impact on the biological features of S. sclerotiorum. This study represents an example of a yadokarivirus trans-encapsidated by an unrelated dsRNA virus, which greatly deepens our knowledge and understanding of the unique life cycles of RNA viruses. IMPORTANCE RNA viruses typically encase their linear genomes in their own capsids. However, a capsidless +ssRNA virus (RnYkV1) highjacks the capsid of a nonsegmented dsRNA virus for the trans-encapsidation of its own RNA and RdRp. RnYkV1 belongs to the family Yadokariviridae, which already contains more than a dozen mycoviruses. However, it is unknown whether other yadokariviruses except RnYkV1 are also hosted by a heterocapsid, although dsRNA viruses with capsid proteins were detected in fungi harboring yadokarivirus. It is noteworthy that almost all presumed partner dsRNA viruses of yadokariviruses belong to the order Ghabrivirales (most probably a totivirus or toti-like virus). Here, we found a capsidless +ssRNA mycovirus, SsYkV1, from hypovirulent strain SCH941 of S. sclerotiorum, and the RNA and RdRp of this mycovirus are trans-encapsidated in virions of a bisegmented dsRNA virus within the free-floating genus Botybirnavirus. Our results greatly expand our knowledge of the unique life cycles of RNA viruses.
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Konstantinidis K, Dovrolis N, Kouvela A, Kassela K, Rosa Freitas MG, Nearchou A, de Courcy Williams M, Veletza S, Karakasiliotis I. Defining Virus-Carrier Networks that Shape the Composition of the Mosquito Core Virome of a Local Ecosystem. Virus Evol 2022; 8:veac036. [PMID: 35505691 PMCID: PMC9055857 DOI: 10.1093/ve/veac036] [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: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 11/21/2022] Open
Abstract
Mosquitoes are the most important vectors of emerging infectious diseases. During the past decade, our understanding of the diversity of viruses they carry has greatly expanded. Most of these viruses are considered mosquito-specific, but there is increasing evidence that these viruses may affect the vector competence of mosquitoes. Metagenomics approaches have focused on specific mosquito species for the identification of what is called the core virome. Despite the fact that, in most ecosystems, multiple species may participate in virus emergence and circulation, there is a lack of understanding of the virus-carrier/host network for both vector-borne and mosquito-specific viruses. Here, we studied the core virome of mosquitoes in a diverse local ecosystem that had 24 different mosquito species. The analysis of the viromes of these 24 mosquito species resulted in the identification of 34 viruses, which included 15 novel viruses, as determined according to the species demarcation criteria of the respective virus families. Most of the mosquito species had never been analysed previously, and a comparison of the individual viromes of the 24 mosquito species revealed novel relationships among mosquito species and virus families. Groups of related viruses and mosquito species from multiple genera formed a complex web in the local ecosystem. Furthermore, analyses of the virome of mixed-species pools of mosquitoes from representative traps of the local ecosystem showed almost complete overlap with the individual-species viromes identified in the study. Quantitative analysis of viruses’ relative abundance revealed a linear relationship to the abundance of the respective carrier/host mosquito species, supporting the theory of a stable core virome in the most abundant species of the local ecosystem. Finally, our study highlights the importance of using a holistic approach to investigating mosquito viromes relationships in rich and diverse ecosystems.
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Affiliation(s)
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Adamantia Kouvela
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Katerina Kassela
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Goreti Rosa Freitas
- Laboratório de Mosquitoes Transmissores de Hematozoários, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andreas Nearchou
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Stavroula Veletza
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
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Abstract
Rhabdoviruses are ubiquitous and diverse viruses that propagate owing to bidirectional interactions with their vertebrate, arthropod, and plant hosts, and some of them could pose global health or agricultural threats. However, rhabdoviruses have rarely been reported in fungi. Here, two newly identified fungal rhabdoviruses, Rhizoctonia solani rhabdovirus 1 (RsRhV1) and RsRhV2, were discovered and molecularly characterized from the phytopathogenic fungus Rhizoctonia solani. The genomic organizations of RsRhV1 and RsRhV2 are 11,716 and 11,496 nucleotides (nt) in length, respectively, and consist of five open reading frames (ORFs) (ORFs I to V). ORF I, ORF IV, and ORF V encode the viral nucleocapsid (N), glycoprotein (G), and RNA polymerase (L), respectively. The putative protein encoded by ORF III has a lower level of identity with the matrix protein of rhabdoviruses. ORF II encodes a hypothetical protein with unknown function. Phylogenetic trees based on multiple alignments of N, L, and G proteins revealed that RsRhV1 and RsRhV2 are new members of the family Rhabdoviridae, but they form an independent evolutionary branch significantly distinct from other known nonfungal rhabdoviruses, suggesting that they represent a novel viral evolutionary lineage within Rhabdoviridae. Compared to strains lacking rhabdoviruses, strains harboring RsRhV2 and RsRhV1 showed hypervirulence, suggesting that RsRhV1 and RsRhV2 might be associated with the virulence of R. solani. Taken together, this study enriches our understanding of the diversity and host range of rhabdoviruses. IMPORTANCE Mycoviruses have been attracting an increasing amount of attention due to their impact on important medical, agricultural, and industrial fungi. Rhabdoviruses are prevalent across a wide spectrum of hosts, from plants to invertebrates and vertebrates. This study molecularly characterized two novel rhabdoviruses from four Rhizoctonia solani strains, based on their genomic structures, transcription strategy, phylogenetic relationships, and biological impact on their host. Our study makes a significant contribution to the literature because it not only enriches the mycovirus database but also expands the known host range of rhabdoviruses. It also offers insight into the evolutionary linkage between animal viruses and mycoviruses and the transmission of viruses from one host to another. Our study will also help expand the contemporary knowledge of the classification of rhabdoviruses, as well as providing a new model to study rhabdovirus-host interactions, which will benefit the agriculture and medical areas of human welfare.
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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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Nuzzo F, Moine A, Nerva L, Pagliarani C, Perrone I, Boccacci P, Gribaudo I, Chitarra W, Gambino G. Grapevine virome and production of healthy plants by somatic embryogenesis. Microb Biotechnol 2022; 15:1357-1373. [PMID: 35182024 PMCID: PMC9049623 DOI: 10.1111/1751-7915.14011] [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: 11/22/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
Abstract
Grapevine (Vitis spp.) is a widespread fruit tree hosting many viral entities that interact with the plant modifying its responses to the environment. The production of virus‐free plants is becoming increasingly crucial for the use of grapevine as a model species in different studies. Using high‐throughput RNA sequencing, the viromes of seven mother plants grown in a germplasm collection vineyard were sequenced. In addition to the viruses and viroids already detected in grapevine, we identified 13 putative new mycoviruses. The different spread among grapevine tissues collected in vineyard, greenhouse and in vitro conditions suggested a clear distinction between viruses/viroids and mycoviruses that can successfully be exploited for their identification. Mycoviruses were absent in in vitro cultures, while plant viruses and viroids were particularly accumulated in these plantlets. Somatic embryogenesis applied to the seven mother plants was effective in the elimination of the complete virome, including mycoviruses. However, different sanitization efficiencies for viroids and grapevine pinot gris virus were observed among genotypes. The absence of mycoviruses in in vitro plantlets, associated with the absence of all viral entities in somaclones, suggested that this regeneration technique is also effective to eradicate endophytic/epiphytic fungi, resulting in gnotobiotic or pseudo‐gnotobiotic plants.
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Affiliation(s)
- Floriana Nuzzo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy
| | - Amedeo Moine
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy
| | - Luca Nerva
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy.,Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, Conegliano, 31015, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy.,Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, Conegliano, 31015, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Strada delle Cacce 73, Torino, 10135, Italy
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Wang Q, Zou Q, Dai Z, Hong N, Wang G, Wang L. Four Novel Mycoviruses from the Hypovirulent Botrytis cinerea SZ-2-3y Isolate from Paris polyphylla: Molecular Characterisation and Mitoviral Sequence Transboundary Entry into Plants. Viruses 2022; 14:v14010151. [PMID: 35062353 PMCID: PMC8777694 DOI: 10.3390/v14010151] [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: 11/27/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
A hypovirulent SZ-2-3y strain isolated from diseased Paris polyphylla was identified as Botrytis cinerea. Interestingly, SZ-2-3y was coinfected with a mitovirus, two botouliviruses, and a 3074 nt fusarivirus, designated Botrytis cinerea fusarivirus 8 (BcFV8); it shares an 87.2% sequence identity with the previously identified Botrytis cinerea fusarivirus 6 (BcFV6). The full-length 2945 nt genome sequence of the mitovirus, termed Botrytis cinerea mitovirus 10 (BcMV10), shares a 54% sequence identity with Fusarium boothii mitovirus 1 (FbMV1), and clusters with fungus mitoviruses, plant mitoviruses and plant mitochondria; hence BcMV10 is a new Mitoviridae member. The full-length 2759 nt and 2812 nt genome sequences of the other two botouliviruses, named Botrytis cinerea botoulivirus 18 and 19 (BcBoV18 and 19), share a 40% amino acid sequence identity with RNA-dependent RNA polymerase protein (RdRp), and these are new members of the Botoulivirus genus of Botourmiaviridae. Horizontal transmission analysis showed that BcBoV18, BcBoV19 and BcFV8 are not related to hypovirulence, suggesting that BcMV10 may induce hypovirulence. Intriguingly, a partial BcMV10 sequence was detected in cucumber plants inoculated with SZ-2-3y mycelium or pXT1/BcMV10 agrobacterium. In conclusion, we identified a hypovirulent SZ-2-3y fungal strain from P. polyphylla, coinfected with four novel mycoviruses that could serve as potential biocontrol agents. Our findings provide evidence of cross-kingdom mycoviral sequence transmission.
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Affiliation(s)
- Qiong Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaoji Dai
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, College of Plant Protection, Hainan University, Ministry of Education, Haikou 570100, China;
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-8728-2130; Fax: +86-27-8738-4670
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Sato Y, Shahi S, Telengech P, Hisano S, Cornejo C, Rigling D, Kondo H, Suzuki N. A new tetra-segmented splipalmivirus with divided RdRP domains from Cryphonectria naterciae, a fungus found on chestnut and cork oak trees in Europe. Virus Res 2022; 307:198606. [PMID: 34688782 DOI: 10.1016/j.virusres.2021.198606] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 01/01/2023]
Abstract
Positive-sense (+), single-stranded (ss) RNA viruses with divided RNA-dependent RNA polymerase (RdRP) domains have been reported from diverse filamentous ascomycetes since 2020. These viruses are termed splipalmiviruses or polynarnaviruses and have been characterized largely at the sequence level, but ill-defined biologically. Cryphonectria naterciae, from which only one virus has been reported, is an ascomycetous fungus potentially plant-pathogenic to chestnut and oak trees. We molecularly characterized multiple viruses in a single Portuguese isolate (C0614) of C. naterciae, taking a metatranscriptomic and conventional double-stranded RNA approach. Among them are a novel splipalmivirus (Cryphonectria naterciae splipalmivirus 1, CnSpV1) and a novel fusagravirus (Cryphonectria naterciae fusagravirus 1, CnFGV1). This study focused on the former virus. CnSpV1 has a tetra-segmented, (+)ssRNA genome (RNA1 to RNA4). As observed for other splipalmiviruses reported in 2020 and 2021, the RdRP domain is separately encoded by RNA1 (motifs F, A and B) and RNA2 (motifs C and D). A hypothetical protein encoded by the 5'-proximal open reading frame of RNA3 shows similarity to a counterpart conserved in some splipalmiviruses. The other RNA3-encoded protein and RNA4-encoded protein show no similarity with known proteins in a blastp search. The tetra-segment nature was confirmed by the conserved terminal sequences of the four CnSpV1 segments (RNA1 to RNA4) and their 100% coexistence in over 100 single conidial isolates tested. The experimental introduction of CnSpV1 along with CnFGV1 into a virus free strain C0754 of C. naterciae vegetatively incompatible with C0614 resulted in no phenotypic alteration, suggesting asymptomatic infection. The protoplast fusion assay indicates a considerably narrow host range of CnSpV1, restricted to the species C. naterciae and C. carpinicola. This study contributes to better understanding of the molecular and biological properties of this unique group of viruses.
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Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Carolina Cornejo
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Sutela S, Piri T, Vainio EJ. Discovery and Community Dynamics of Novel ssRNA Mycoviruses in the Conifer Pathogen Heterobasidion parviporum. Front Microbiol 2021; 12:770787. [PMID: 34899655 PMCID: PMC8652122 DOI: 10.3389/fmicb.2021.770787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Heterobasidion species are highly destructive basidiomycetous conifer pathogens of the Boreal forest region. Earlier studies have revealed dsRNA virus infections of families Curvulaviridae and Partitiviridae in Heterobasidion strains, and small RNA deep sequencing has also identified infections of Mitoviridae members in these fungi. In this study, the virome of Heterobasidion parviporum was examined for the first time by RNA-Seq using total RNA depleted of rRNA. This method successfully revealed new viruses representing two established (+)ssRNA virus families not found earlier in Heterobasidion: Narnaviridae and Botourmiaviridae. In addition, we identified the presence of a recently described virus group tentatively named “ambiviruses” in H. parviporum. The H. parviporum isolates included in the study originated from experimental forest sites located within 0.7 km range from each other, and a population analysis including 43 isolates was conducted at one of the experimental plots to establish the prevalence of the newly identified viruses in clonally spreading H. parviporum individuals. Our results indicate that viral infections are considerably more diverse and common among Heterobasidion isolates than known earlier and include ssRNA viruses with high prevalence and interspecies variation.
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Affiliation(s)
- Suvi Sutela
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tuula Piri
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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Khan HA, Shamsi W, Jamal A, Javaied M, Sadiq M, Fatma T, Ahmed A, Arshad M, Waseem M, Babar S, Dogar MM, Virk N, Janjua HA, Kondo H, Suzuki N, Bhatti MF. Assessment of mycoviral diversity in Pakistani fungal isolates revealed infection by 11 novel viruses of a single strain of Fusarium mangiferae isolate SP1. J Gen Virol 2021; 102. [PMID: 34850675 DOI: 10.1099/jgv.0.001690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.
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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, 44000, Islamabad, Pakistan.,Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Wajeeha Shamsi
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Memoona Javaied
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mashal Sadiq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Maleeha Arshad
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mubashra Waseem
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Samra Babar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Midhat Mustafa Dogar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: EBS Universität für Wirtschaft und Recht, EBS Business School, Rheingaustrasse 1, 65375, Oestrich-Winkel, Germany
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
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Jia J, Mu F, Fu Y, Cheng J, Lin Y, Jiang D, Xie J. Characterization of a newly identified RNA segment derived from the genome of Sclerotinia sclerotiorum reovirus 1. Arch Virol 2021; 167:603-606. [PMID: 34855005 DOI: 10.1007/s00705-021-05319-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/18/2021] [Indexed: 11/28/2022]
Abstract
Sclerotinia sclerotiorum reovirus 1 (SsReV1) was previously reported to infect hypovirulent strain SCH941 of the phytopathogenic fungus Sclerotinia sclerotiorum and to contain 11 double-stranded RNA (dsRNA) segments (S1-S11). Here, we report that SsReV1 is actually composed of 12 dsRNA segments instead of 11. The full-length nucleotide sequence of the twelfth segment (S12) was determined using a combination of RACE and high-throughput sequencing methods. S12 is 1217 nucleotides in length and has highly conserved terminal sequences that resemble those of the other 11 segments of SsReV1. S12 contains a single open reading frame encoding a protein (VP12) of 311 amino acids. Although regular BLAST analysis did not reveal any similarity of VP12 to known sequences, it was found to be homologous to the VP11 of Colorado tick fever virus of the genus Coltivirus when a hidden-Markov-model-based HHpred analysis was performed. A single-protoplast regeneration experiment suggested that S12 and S2 were maintained or lost in parallel. In summary, the SsReV1 genome consists of 12 dsRNA segments.
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Affiliation(s)
- Jichun Jia
- 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
| | - Fan Mu
- 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
| | - 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
| | - 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
| | - 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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Liang W, Lu Z, Duan J, Jiang D, Xie J, Cheng J, Fu Y, Chen T, Li B, Yu X, Chen W, Lin Y. A novel alphahypovirus that infects the fungal plant pathogen Sclerotinia sclerotiorum. Arch Virol 2021; 167:213-217. [PMID: 34826002 DOI: 10.1007/s00705-021-05315-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022]
Abstract
A novel positive single-stranded RNA virus, Sclerotinia sclerotiorum hypovirus 9 (SsHV9), was identified in the plant-pathogenic Sclerotinia sclerotiorum strain GB375, which was associated with a garden bean plant in the United States. The complete genome of SsHV9 is 14,067 nucleotides in length, excluding the poly(A) tail. It has a single large open reading frame encoding a putative polyprotein (4,196 amino acids), which is predicted to contain a papain-like protease, a protein of unknown function, an RNA-dependent RNA polymerase, and an RNA helicase. Phylogenetic analysis based on a multiple alignment of amino acid sequences of polyproteins that suggested SsHV9 belongs to the proposed genus "Alphahypovirus" in the family Hypoviridae.
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Affiliation(s)
- Weibo Liang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Zhongbo Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jie Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiasen Cheng
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Weidong Chen
- US Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, Washington, 99164, USA
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
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47
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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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Wang Z, Neupane A, Feng J, Pedersen C, Lee Marzano SY. Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome. Viruses 2021; 13:v13091867. [PMID: 34578448 PMCID: PMC8473204 DOI: 10.3390/v13091867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/30/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Sunflowers (Helianthus annuus L.) are susceptible to multiple diseases in field production. In this study, we collected diseased sunflower leaves in fields located in South Dakota, USA, for virome investigation. The leaves showed visible symptoms on the foliage, indicating phomopsis and rust infections. To identify the viruses potentially associated with the disease diagnosed, symptomatic leaves were obtained from diseased plants. Total RNA was extracted corresponding to each disease diagnosed to generate libraries for paired-end high throughput sequencing. Short sequencing reads were assembled de novo and the contigs with similarities to viruses were identified by aligning against a custom protein database. We report the discovery of two novel mitoviruses, four novel partitiviruses, one novel victorivirus, and nine novel totiviruses based on similarities to RNA-dependent RNA polymerases and capsid proteins. Contigs similar to bean yellow mosaic virus and Sclerotinia sclerotiorum hypovirulence-associated DNA virus were also detected. To the best of our knowledge, this is the first report of direct metatranscriptomics discovery of viruses associated with fungal infections of sunflowers bypassing culturing. These newly discovered viruses represent a natural genetic resource from which we can further develop potential biopesticide to control sunflower diseases.
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Affiliation(s)
- Ziyi Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (Z.W.); (A.N.); (C.P.)
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (Z.W.); (A.N.); (C.P.)
| | - Jiuhuan Feng
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA;
| | - Connor Pedersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (Z.W.); (A.N.); (C.P.)
- United States Department of Agriculture-Agricultural Research Service, Toledo, OH 43606, USA
| | - Shin-Yi Lee Marzano
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (Z.W.); (A.N.); (C.P.)
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA;
- United States Department of Agriculture-Agricultural Research Service, Toledo, OH 43606, USA
- Correspondence: ; Tel.: +1-419-530-5053
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49
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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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50
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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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