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Prajapati MR, Diksha D, Thapa P, Sharma SK, Gupta N, Baranwal VK. Identification of a novel mitovirus in grapevine through high-throughput sequencing. Int Microbiol 2024:10.1007/s10123-024-00572-0. [PMID: 39155336 DOI: 10.1007/s10123-024-00572-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/17/2024] [Accepted: 08/01/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome. METHODS AND RESULTS Here, we identify putative novel mitovirus, grapevine mitovirus 1 (GMV1) through high-throughput sequencing (HTS) of grapevine rootstocks (Vitis spp.), and the identified virus was confirmed using virus-specific primers in RT-PCR assay. The genomic RNA of GMV1 encodes complete open reading frame (ORF) of 2,496 nucleotides (nts) in length. RNA-dependent RNA polymerase (RdRp) encoded by the viral genome contained one RdRp conserved domain. BLASTx analysis of GMV1 genome showed sequence identity of 33.18-56.75% with the existing mitovirus sequences. Phylogenetic analysis based on genome sequences showed that GMV1 clustered in a distinct clade to other mitoviruses. CONCLUSION Grapevine mitovirus 1 represents a newly discovered species within the Unuamitovirus genus of the Mitoviridae family, targeting fungal mitochondria. While the majority of recognized mitoviruses typically lack a functional RdRp as per the plant mitochondrial genetic code, GMV1 encodes a complete RdRp in accordance with both fungal and plant mitochondrial genetic codes.
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Affiliation(s)
- Malyaj R Prajapati
- Advanced Center for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Damini Diksha
- Advanced Center for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Pooja Thapa
- Advanced Center for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Susheel Kumar Sharma
- Advanced Center for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012.
| | - Nitika Gupta
- Advanced Center for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Virendra Kumar Baranwal
- Advanced Center for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012.
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2
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Xin P, Chaoqun X, Chaojie L, Shuwei Y, Tiantian L, Junli D, Xiaoting Z, Honglian L, Jianhua L, Fei G. Molecular characterization of a new botybirnavirus that infects Alternaria sp. from tobacco. Arch Virol 2024; 169:149. [PMID: 38888750 DOI: 10.1007/s00705-024-06072-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: 10/27/2023] [Accepted: 05/07/2024] [Indexed: 06/20/2024]
Abstract
The genus Alternaria comprises many important fungal pathogens that infect a wide variety of organisms. In this report, we present the discovery of a new double-stranded RNA (dsRNA) mycovirus called Alternaria botybirnavirus 2 (ABRV2) from a phytopathogenic strain, XC21-21C, of Alternaria sp. isolated from diseased tobacco leaves in China. The ABRV2 genome consists of two dsRNA components, namely dsRNA1 and dsRNA2, with lengths of 6,162 and 5,865 base pairs (bp), respectively. Each of these genomic dsRNAs is monocistronic, encoding hypothetical proteins of 201.6 kDa (P1) and 2193.3 kDa (P2). ABRV2 P1 and P2 share 50.54% and 63.13% amino acid sequence identity with the corresponding proteins encoded by dsRNA1 of Alternaria botybirnavirus 1 (ABRV1). Analysis of its genome organization and phylogenetic analysis revealed that ABRV2 is a new member of the genus Botybirnavirus.
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Affiliation(s)
- Pan Xin
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Xue Chaoqun
- Zhengzhou Tobacco Research Institute of CNTC, 450001, Zhengzhou, China
| | - Liu Chaojie
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Yan Shuwei
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Lv Tiantian
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Dai Junli
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Zhang Xiaoting
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Li Honglian
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China
| | - Li Jianhua
- Xuchang Tobacco Company of Henan Province, 461000, Xuchang, China.
| | - Gao Fei
- College of Plant Protection, Henan Agricultural University, 450002, Zhengzhou, China.
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3
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Yu D, Wang Q, Song W, Kang Y, Lei Y, Wang Z, Chen Y, Huai D, Wang X, Liao B, Yan L. Characterization of Two Novel Single-Stranded RNA Viruses from Agroathelia rolfsii, the Causal Agent of Peanut Stem Rot. Viruses 2024; 16:854. [PMID: 38932147 PMCID: PMC11209298 DOI: 10.3390/v16060854] [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: 04/06/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Peanut stem rot is a soil-borne disease caused by Agroathelia rolfsii. It occurs widely and seriously affects the peanut yield in most peanut-producing areas. The mycoviruses that induce the hypovirulence of some plant pathogenic fungi are potential resources for the biological control of fungal diseases in plants. Thus far, few mycoviruses have been found in A. rolfsii. In this study, two mitoviruses, namely, Agroathelia rolfsii mitovirus 1 (ArMV1) and Agroathelia rolfsii mitovirus 2 (ArMV2), were identified from the weakly virulent A. rolfsii strain GP3-1, and they were also found in other A. rolfsii isolates. High amounts of ArMV1 and ArMV2in the mycelium could reduce the virulence of A. rolfsii strains. This is the first report on the existence of mitoviruses in A. rolfsii. The results of this study may provide insights into the classification and evolution of mitoviruses in A. rolfsii and enable the exploration of the use of mycoviruses as biocontrol agents for the control of peanut stem rot.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Boshou Liao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural and Rural Affairs, Wuhan 430062, China; (D.Y.); (Q.W.); (W.S.); (Y.K.); (Y.L.); (Z.W.); (Y.C.); (D.H.); (X.W.)
| | - Liying Yan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural and Rural Affairs, Wuhan 430062, China; (D.Y.); (Q.W.); (W.S.); (Y.K.); (Y.L.); (Z.W.); (Y.C.); (D.H.); (X.W.)
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4
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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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5
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Ye L, Shi X, He Y, Chen J, Xu Q, Shafik K, Fu L, Yin Y, Kotta-Loizou I, Xu W. A novel botybirnavirus with a unique satellite dsRNA causes latent infection in Didymella theifolia isolated from tea plants. Microbiol Spectr 2023; 11:e0003323. [PMID: 37962342 PMCID: PMC10714997 DOI: 10.1128/spectrum.00033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/02/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE A novel botybirnavirus, infecting the tea plant pathogen Didymella theifolia and tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1), together with an additional double-stranded RNA (dsRNA), was characterized. DtBRV1 comprises two dsRNAs (1 and 2) encapsidated in isometric virions, while dsRNA3 is a satellite. The satellite represents a unique specimen since it contains a duplicated region and has high similarity to the two botybirnavirus dsRNAs, supporting the notion that it most likely originated from a deficient genomic component. The biological characteristics of DtBRV1 were further determined. With their unique molecular traits, DtBRV1 and its related dsRNA expand our understanding of virus diversity, taxonomy, and evolution.
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Affiliation(s)
- Liangchao Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Xinyu Shi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Yunqiang He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Jiao Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Qingeng Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Karim Shafik
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Lanning Fu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Yumeng Yin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Wenxing Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
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6
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Lopez-Jimenez J, Herrera J, Alzate JF. Expanding the knowledge frontier of mitoviruses in Cannabis sativa. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105523. [PMID: 37940011 DOI: 10.1016/j.meegid.2023.105523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/25/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within the Cannabaceae family. Cannabis sativa has been in the spotlight in recent years due to the growing industrial applications of plant derivatives, such as fiber and secondary metabolites. Given the importance of Cannabis in today's agriculture, our study aimed to expand the knowledge frontier of Mitoviruses in C. sativa by increasing the number of reference genomes of CasaMV1 available in public databases and representing a larger number of crops in countries where its industrial-scale growth is legalized. To achieve this goal, we used transcriptomics to sequence the first mitoviral genomes of Colombian crops and analyzed RNA-seq datasets available in the SRA databank. Additionally, the evolutionary analysis performed using the mitovirus genomes revealed two main lineages of CasaMV1, termed CasaMV1_L1 and CasaMV1_L2. These mitoviral lineages showed strong clustering based on the geographic location of the crops and differential expression intensities.
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Affiliation(s)
- Juliana Lopez-Jimenez
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Jorge Herrera
- Fábrica de Plantas y Semillas de Antioquia S.A.S. - FASPLAN, El Carmen de Viboral, Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia; Fábrica de Plantas y Semillas de Antioquia S.A.S. - FASPLAN, El Carmen de Viboral, Antioquia, Colombia; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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7
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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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Hough B, Steenkamp E, Wingfield B, Read D. Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses. Viruses 2023; 15:1202. [PMID: 37243288 PMCID: PMC10224137 DOI: 10.3390/v15051202] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.
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Affiliation(s)
| | | | - Brenda Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria 0002, South Africa; (B.H.); (E.S.); (D.R.)
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9
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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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10
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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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11
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A Botybirnavirus Isolated from Alternaria tenuissima Confers Hypervirulence and Decreased Sensitivity of Its Host Fungus to Difenoconazole. Viruses 2022; 14:v14102093. [DOI: 10.3390/v14102093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022] Open
Abstract
Alternaria alternata botybirnavirus 1 (AaBRV1) was isolated from a strain of Alternaria alternata, causing watermelon leaf blight in our previous research. The effect of AaBRV1 on the phenotype of its host fungus, however, was not determined. In the present study, a novel strain of AaBRV1 was identified in A. tenuissima strain TJ-NH-51S-4, the causal agent of cotton Alternaria leaf spot, and designated as AaBRV1-AT1. A mycovirus AaBRV1-AT1-free strain TJ-NH-51S-4-VF was obtained by protoplast regeneration, which eliminated AaBRV1-AT1 from the mycovirus AaBRV1-AT1-infected strain TJ-NH-51S-4. Colony growth rate, spore production, and virulence of strain TJ-NH-51S-4 were greater than they were in TJ-NH-51S-4-VF, while the sensitivity of strain TJ-NH-51S-4 to difenoconazole, as measured by the EC50, was lower. AaBRV1-AT1 was capable of vertical transmission via asexual spores and horizontal transmission from strain TJ-NH-51S-4 to strain XJ-BZ-5-1hyg (another strain of A. tenuissima) through hyphal contact in pairing cultures. A total of 613 differentially expressed genes (DEGs) were identified in a comparative transcriptome analysis between TJ-NH-51S-4 and TJ-NH-51S-4-VF. Relative to strain TJ-NH-51S-4-VF, the number of up-regulated and down-regulated DEGs in strain TJ-NH-51S-4 was 286 and 327, respectively. Notably, the expression level of one DEG-encoding cytochrome P450 sterol 14α-demethylase and four DEGs encoding siderophore iron transporters were significantly up-regulated. To our knowledge, this is the first documentation of hypervirulence and reduced sensitivity to difenoconazole induced by AaBRV1-AT1 infection in A. tenuissima.
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Six Novel Mycoviruses Containing Positive Single-Stranded RNA and Double-Stranded RNA Genomes Co-Infect a Single Strain of the Rhizoctoniasolani AG-3 PT. Viruses 2022; 14:v14040813. [PMID: 35458543 PMCID: PMC9025235 DOI: 10.3390/v14040813] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 12/10/2022] Open
Abstract
Six novel mycoviruses that collectively represent the mycovirome of Rhizoctonia solani anastomosis group (AG)-3 PT strain ZJ-2H, which causes potato black scurf, were identified through metatranscriptome sequencing and putatively designated as Rhizoctonia solani fusarivirus 4 [RsFV4, positive single-stranded RNA (+ssRNA)], Rhizoctonia solani fusarivirus 5 (RsFV5, +ssRNA), Rhizoctonia solani mitovirus 40 (RsMV40, +ssRNA), Rhizoctonia solani partitivirus 10 [RsPV10, double-stranded RNA (dsRNA)], Rhizoctonia solani partitivirus 11 (RsPV11, dsRNA), and Rhizoctonia solani RNA virus 11 (RsRV11, dsRNA). Whole genome sequences of RsFV4, RsMV40, RsPV10, RsPV11, and RsRV11, as well as a partial genome sequence of RsFV5, were obtained. The 3'- and 5'- untranslated regions of the five mycoviruses with complete genome sequences were folded into stable stem-loop or panhandle secondary structures. RsFV4 and RsFV5 are most closely related to Rhizoctonia solani fusarivirus 1 (RsFV1), however, the first open reading frame (ORF) of RsFV4 and RsFV5 encode a hypothetical protein that differs from the first ORF of RsFV1, which encodes a helicase. We confirmed that RsPV10 and RsPV11 assemble into the spherical virus particles (approximately 30 nm in diameter) that were extracted from strain ZJ-2H. This is the first report that +ssRNA and dsRNA viruses co-infect a single strain of R. solani AG-3 PT.
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Chen Z, Chen L, Anane RF, Wang Z, Gao L, Li S, Wen G, Yu D, Zhao M. Complete genome sequence of a novel mitovirus detected in Paris polyphylla var. yunnanensis. Arch Virol 2022; 167:645-650. [PMID: 35037104 DOI: 10.1007/s00705-021-05339-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
Paris mitovirus 1 (ParMV1) is a positive-sense RNA virus that was detected in diseased Paris polyphylla var. yunnanensis plants in Wenshan, Yunnan. The complete genome sequence of ParMV1 is 2,751 nucleotides in length, and the genome structure is typical of mitoviruses. The ParMV1 genome has a single open reading frame (ORF; nt 358-2,637) that encodes an RNA-dependent RNA polymerase (RdRp) with a predicted molecular mass of 86.42 kDa. ParMV1 contains six conserved motifs (Ι-VΙ) that are unique to mitoviruses. The 5' and 3' termini of the genome are predicted to have a stable secondary structure, with the reverse complementary sequence forming a panhandle structure. Comparative genome analysis revealed that the RdRp of ParMV1 shares 23.1-40.6% amino acid (aa) and 32.3-45.7% nucleotide (nt) sequence identity with those of other mitoviruses. Phylogenetic analysis based on RdRp aa sequences showed that ParMV1 clusters with mitoviruses and hence should be considered a new member of the genus Mitovirus in the family Mitoviridae. This is the first report of a novel mitovirus infecting Paris polyphylla var. yunnanensis.
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Affiliation(s)
- Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Lu Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Rex Frimpong Anane
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.,State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Zhe Wang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Like Gao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Guosong Wen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China
| | - Daihong Yu
- Plant Protection and Quarantine Station of Yuanjiang County, Yuxi, 653300, Yunnan, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China. .,Research & Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, 32 Jiaochang Donglu, Kunming, 650201, Yunnan, China.
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Shafik K, Umer M, You H, Aboushedida H, Wang Z, Ni D, Xu W. Characterization of a Novel Mitovirus Infecting Melanconiella theae Isolated From Tea Plants. Front Microbiol 2021; 12:757556. [PMID: 34867881 PMCID: PMC8635788 DOI: 10.3389/fmicb.2021.757556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
A dsRNA segment was identified in the fungus Melanconiella theae isolated from tea plants. The complete dsRNA sequence, determined by random cloning together with RACE protocol, is 2,461 bp in length with an AU-rich content (62.37%) and comprises a single ORF of 2,265-nucleotides encoding an RNA-dependent RNA-polymerase (RdRp, 754 amino acids in size). The terminus sequences can fold into predicted stable stem-loop structures. A BLASTX and phylogenetic analysis revealed the dsRNA genome shows similarities with the RdRp sequences of mitoviruses, with the highest identity of 48% with those of grapevine-associated mitovirus 20 and Colletotrichum fructicola mitovirus 1. Our results reveal a novel member, tentatively named Melanconiella theae mitovirus 1 (MtMV1), belongs to the family Mitoviridae. MtMV1 is capsidless as examined by transmission electron microscope, efficiently transmitted through conidia as 100 conidium-generated colonies were analyzed, and easily eliminated by hyphal tipping method combined with green-leaf tea powder. MtMV1 has a genomic sequence obviously divergent from those of most members in the family Mitoviridae and some unique characteristics unreported in known members. This is the first report of a mycovirus infecting Melanconiella fungi to date.
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Affiliation(s)
- Karim Shafik
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Umer
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huafeng You
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hamdy Aboushedida
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhenhua Wang
- Technology Center of Wuhan Customs District, Wuhan, China
| | - Dejiang Ni
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Wenxing Xu
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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15
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Wang H, Liu H, Zhou Q. The complete genome sequence of a new mitovirus from the phytopathogenic fungus Colletotrichum higginsianum. Arch Virol 2021; 166:1481-1484. [PMID: 33616726 DOI: 10.1007/s00705-021-04996-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/27/2020] [Indexed: 02/07/2023]
Abstract
In this study, a novel mitovirus designed "Colletotrichum higginsianum mitovirus 1" (ChMV1) was isolated from the phytopathogenic fungus Colletotrichum higginsianum. The genome of this mitovirus is 2,893 nt in length with an A + U content of 61% and contains a large open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). A BLASTp analysis revealed that the RdRp domain of ChMV1 had 30.25% to 61.72% sequence identity to those of members of the genus Mitovirus and showed the highest degree of similarity (61.72% identity) to Botrytis cinerea mitovirus 3 (BcMV3). Phylogenetic analysis further indicated that ChMV1 is a member in the genus Mitovirus of the family Mitoviridae. To the best of our knowledge, this is the first report of a mitovirus in C. higginsianum.
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Affiliation(s)
- Hui Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Hong Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
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Liu H, Liu M, Zhu H, Zhong J, Liao X, Zhou Q. Molecular characterization of a novel mitovirus from the plant‑pathogenic fungus Botryosphaeria dothidea. Arch Virol 2021; 166:633-637. [PMID: 33222011 DOI: 10.1007/s00705-020-04886-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/02/2020] [Indexed: 02/03/2023]
Abstract
Here, a novel mycovirus, Botryosphaeria dothidea mitovirus 1 (BdMV1), was isolated from a phytopathogenic fungus, Botryosphaeria dothidea, and its molecular characteristics were determined. BdMV1 has a genome of 2,667 nt that contains a single large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes an RNA-dependent RNA polymerase (RdRp) of 727 amino acids with a molecular mass of 81.64 kDa. BLASTp analysis revealed that the RdRp domain of BdMV1 has 39.59% and 39.18% sequence identity to Plasmopara viticola associated mitovirus 43 and Setosphaeria turcica mitovirus 1, respectively. Phylogenetic analysis further suggested that BdMV1 is a new member of the genus Mitovirus within the family Mitoviridae. To the best of our knowledge, this is the first report of a mitovirus in B. dothidea.
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Affiliation(s)
- Hong Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Miao Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Hongjian Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Xiaolan Liao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
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Wang J, Ni Y, Liu X, Zhao H, Xiao Y, Xiao X, Li S, Liu H. Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents. Virus Evol 2020; 7:veaa095. [PMID: 33505706 PMCID: PMC7816680 DOI: 10.1093/ve/veaa095] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Macrophomina phaseolina is an important necrotrophic phytopathogenic fungus and cause extensive damage in many oilseed crops. Twelve M.phaseolina isolates with diverse biological phenotypes were selected for a high-throughput sequencing-based metatranscriptomic and bioinformatics analysis to identify viruses infecting M.phaseolina. The analysis identified 40 partial or nearly complete viral genome segments, 31 of which were novel viruses. Among these viral sequences, 43% of the viral genomes were double-stranded RNA (dsRNA), 47% were positive single-stranded RNA (ssRNA+), and the remaining 10% were negative sense-stranded RNA (ssRNA−). The 40 viruses showed affinity to 13 distinct viral lineages, including Bunyavirales (four viruses), Totiviridae (three viruses), Chrysoviridae (five viruses), Partitiviridae (four viruses), Hypoviridae (one virus), Endornaviridae (two viruses), Tombusviridae (three viruses), Narnaviridae (one virus), Potyviridae (one virus), Bromoviridae (one virus), Virgaviridae (six viruses), ‘Fusagraviridae’ (five viruses), and Ourmiavirus (four viruses). Two viruses are closely related to two families, Potyviridae and Bromoviridae, which previously contained no mycovirus species. Moreover, nine novel viruses associated with M.phaseolina were identified in the family Totiviridae, Endornaviridae, and Partitiviridae. Coinfection with multiple viruses is prevalent in M.phaseolina, with each isolate harboring different numbers of viruses, ranging from three to eighteen. Furthermore, the effects of the viruses on the fungal host were analyzed according to the biological characteristics of each isolate. The results suggested that M.phaseolina hypovirus 2, M.phaseolina fusagravirus virus 1-5 (MpFV1-5), M.phaseolina endornavirus 1-2 (MpEV1-2), M.phaseolina ourmia-like virus 1-3 (MpOLV1-3), M.phaseolina mitovirus 4 (MpMV4), and M.phaseolina mycobunyavirus 1-4 (MpMBV1-4) were only detected in hypovirulent isolates. Those viruses associated with hypovirulence might be used as biological control agents as an environmentally friendly alternative to chemical fungicides. These findings considerably expand our understanding of mycoviruses in M.phaseolina and unvailed the presence of a huge difference among viruses in isolates from different hosts in distant geographical regions. Together, the present study provides new knowledge about viral evolution and fungus-virus coevolution.
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Affiliation(s)
- Jing Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China.,Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Yannong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province, PR China
| | - Xueqiong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province, PR China
| | - Shujun Li
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
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Li S, Li Y, Hu C, Han C, Zhou T, Zhao C, Wu X. Full genome sequence of a new mitovirus from the phytopathogenic fungus Rhizoctonia solani. Arch Virol 2020; 165:1719-1723. [PMID: 32424446 DOI: 10.1007/s00705-020-04664-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/05/2020] [Indexed: 12/14/2022]
Abstract
A double-stranded RNA (dsRNA) segment was identified in Rhizoctonia solani anastomosis group (AG)-2-2IIIB, the primary causal agent of Rhizoctonia crown and root rot of sugar beet. The dsRNA segment represented the genome replication intermediate of a new mitovirus that was tentatively designated as "Rhizoctonia solani mitovirus 39" (RsMV-39). The complete sequence of the dsRNA was 2805 bp in length with 61.9% A+U content. Using either the fungal mitochondrial or universal genetic code, a protein of 840 amino acids containing an RNA-dependent RNA polymerase (RdRp) domain was predicted with a molecular mass of 94.46 kDa. BLASTp analysis revealed that the RdRp domain of RsMV-39 had 43.55% to 72.96% sequence identity to viruses in the genus Mitovirus, and was the most similar (72.96% identical) to that of Ceratobasidium mitovirus A (CbMV-A). Phylogenetic analysis based on RdRp domains clearly showed that RsMV-39 is a member of a distinct species in the genus Mitovirus of the family Mitoviridae. This is the first full genome sequence of a mycovirus associated with R. solani AG-2-2IIIB.
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Affiliation(s)
- Siwei Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Yuting Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Chenghui Hu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Tao Zhou
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Can Zhao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
- College of Horticulture, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
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Viruses Infecting the Plant Pathogenic Fungus Rhizoctonia solani. Viruses 2019; 11:v11121113. [PMID: 31801308 PMCID: PMC6950361 DOI: 10.3390/v11121113] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/18/2019] [Accepted: 11/26/2019] [Indexed: 12/15/2022] Open
Abstract
The cosmopolitan fungus Rhizoctonia solani has a wide host range and is the causal agent of numerous crop diseases, leading to significant economic losses. To date, no cultivars showing complete resistance to R. solani have been identified and it is imperative to develop a strategy to control the spread of the disease. Fungal viruses, or mycoviruses, are widespread in all major groups of fungi and next-generation sequencing (NGS) is currently the most efficient approach for their identification. An increasing number of novel mycoviruses are being reported, including double-stranded (ds) RNA, circular single-stranded (ss) DNA, negative sense (−)ssRNA, and positive sense (+)ssRNA viruses. The majority of mycovirus infections are cryptic with no obvious symptoms on the hosts; however, some mycoviruses may alter fungal host pathogenicity resulting in hypervirulence or hypovirulence and are therefore potential biological control agents that could be used to combat fungal diseases. R. solani harbors a range of dsRNA and ssRNA viruses, either belonging to established families, such as Endornaviridae, Tymoviridae, Partitiviridae, and Narnaviridae, or unclassified, and some of them have been associated with hypervirulence or hypovirulence. Here we discuss in depth the molecular features of known viruses infecting R. solani and their potential as biological control agents.
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Wang Q, Cheng S, Xiao X, Cheng J, Fu Y, Chen T, Jiang D, Xie J. Discovery of Two Mycoviruses by High-Throughput Sequencing and Assembly of Mycovirus-Derived Small Silencing RNAs From a Hypovirulent Strain of Sclerotinia sclerotiorum. Front Microbiol 2019; 10:1415. [PMID: 31338072 PMCID: PMC6626909 DOI: 10.3389/fmicb.2019.01415] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/05/2019] [Indexed: 11/24/2022] Open
Abstract
Sclerotinia sclerotiorum, an important phytopathogenic fungus, harbors rich diversity of mycoviruses. Lately, more mycoviruses can be successfully and accurately discovered by deep sequencing, especially those that could not be detected by traditional double-stranded RNA (dsRNA) extraction. Previously, we reported that the hypovirulent S. sclerotiorum strain SZ-150 is coinfected by Sclerotinia sclerotiorum hypovirus 1 (SsHV1) and its related satellite RNA. Here, aside from SsHV1, we detected two other mycoviruses, Sclerotinia sclerotiorum botybirnavirus 3 (SsBV3/SZ-150) and Sclerotinia sclerotiorum mycotymovirus 1 (SsMTV1/SZ-150), coinfecting strain SZ-150, by deep sequencing and assembly of mycovirus-derived small RNAs and determined their full-length genomes. The genome of SsBV3/SZ-150 was found to be composed of two linear dsRNA segments, 6,212, and 5,880 bp in size, respectively. Each dsRNA segment of SsBV3/SZ-150 contains a large open reading frame (ORF) encoding RNA-dependent RNA polymerase (RdRp) and a hypothetical protein. The whole genome of SsBV3/SZ-150 shares more than 95% sequence identity with Botrytis porri botybirnavirus 1 (BpBV1) at the nucleotide (nt) or amino acid level. Thus, SsBV3/SZ-150 was assumed to be a strain of BpBV1. The genome of SsMTV1/SZ-150 consists of 6,391 nt excluding the poly(A) tail. SsMTV1/SZ-150 was predicted to contain a large ORF that encodes a putative replication-associated polyprotein (RP) with three conserved domains of viral RNA methyltransferase, viral RNA helicase, and RdRp. Phylogenetic analyses suggest that SsMTV1/SZ-150 is related, albeit distantly, to members of the family Tymoviridae. Analysis of the small RNAs derived from SsBV3/SZ-150 and SsMTV1/SZ-150 revealed that small-RNA lengths mainly range from 20 to 24 nt, with a peak at 22 nt, and the most abundant 5′-terminal nucleotide is uridine, suggesting that the Dicer 2 and Argonaute 1, two key components in the RNA inference pathway, may play important roles in the resistance to mycoviral infection in S. sclerotiorum. Neither SsBV3/SZ-150 nor SsMTV1/SZ-150 is a causal agent of hypovirulence in strain SZ-150.
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Affiliation(s)
- Qianqian Wang
- 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
| | - Shufen 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
| | - Xueqiong Xiao
- 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
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- 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
| | - 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
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21
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Thapa V, Roossinck MJ. Determinants of Coinfection in the Mycoviruses. Front Cell Infect Microbiol 2019; 9:169. [PMID: 31179246 PMCID: PMC6542947 DOI: 10.3389/fcimb.2019.00169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Vaskar Thapa
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, United States
| | - Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, United States
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22
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Shamsi W, Sato Y, Jamal A, Shahi S, Kondo H, Suzuki N, Bhatti MF. Molecular and biological characterization of a novel botybirnavirus identified from a Pakistani isolate of Alternaria alternata. Virus Res 2019; 263:119-128. [DOI: 10.1016/j.virusres.2019.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 11/15/2022]
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23
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Characterization of a Botybirnavirus Conferring Hypovirulence in the Phytopathogenic Fungus Botryosphaeria dothidea. Viruses 2019; 11:v11030266. [PMID: 30884907 PMCID: PMC6466033 DOI: 10.3390/v11030266] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 01/12/2023] Open
Abstract
A double-stranded RNA (dsRNA) virus was isolated and characterized from strain EW220 of the phytopathogenic fungus Botryosphaeria dothidea. The full-length cDNAs of the dsRNAs were 6434 bp and 5986 bp in size, respectively. The largest dsRNA encodes a cap-pol fusion protein that contains a coat protein gene and an RNA-dependent RNA polymerase (RdRp) domain, and the second dsRNA encodes a hypothetical protein. Genome sequence analysis revealed that the sequences of the dsRNA virus shared 99% identity with Bipolaris maydis botybirnavirus 1(BmBRV1) isolated from the causal agent of corn southern leaf blight, Bipolaris maydis. Hence, the dsRNA virus constitutes a new strain of BmBRV1 and was named Bipolaris maydis botybirnavirus 1 strain BdEW220 (BmBRV1-BdEW220). BmBRV1-BdEW220 contains spherical virions that are 37 nm in diameter and consist of two dsRNA segments. The structural proteins of the BmBRV1-BdEW220 virus particles were 110 kDa, 90 kDa, and 80 kDa and were encoded by dsRNA1 and 2-ORFs. Phylogenetic reconstruction indicated that BmBRV1 and BmBRV1-BdEW220 are phylogenetically related to the genus Botybirnavirus. Importantly, BmBRV1-BdEW220 influences the growth of B. dothidea and confers hypovirulence to the fungal host. To our knowledge, this is the first report of a botybirnavirus in B. dothidea.
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Cottet L, Potgieter CA, Castro ME, Castillo A. Molecular characterization of a new botybirnavirus that infects Botrytis cinerea. Arch Virol 2019; 164:1479-1483. [PMID: 30848387 DOI: 10.1007/s00705-019-04184-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Eight different double-stranded RNA (dsRNA) molecules were found in the wild-type fungal strain Botrytis cinerea CCg427. The electrophoretic profile displayed molecules with approximate sizes of 1, 1.3, 1.6, 1.8, 3.3, 4.1, 6.5, and 12 kbp. Sequences analysis of the molecules in the 6.5-kbp band revealed the presence of two different dsRNA molecules (dsRNA-1 and dsRNA-2) of 6192 and 5567 bp. Each molecule contained a unique ORF (5487 and 4836 nucleotides in dsRNA-1 and dsRNA-2, respectively). The ORF of dsRNA-1 encodes a 205-kDa polypeptide that shares 58% amino acid sequence identity with the RNA-dependent RNA polymerase (RdRp) encoded by dsRNA-1 of Alternaria sp. SCFS-3 botybirnavirus (ABRV1), whereas the ORF of dsRNA-2 encodes a 180-kDa polypeptide that shares 52% amino acid sequence identity with an unclassified protein encoded by dsRNA-2 of ABRV1. Genome organization and phylogenetic analysis based on the amino acid sequences of RdRps in members of different dsRNA virus families showed that the dsRNAs in the 6.5-kbp band correspond to the genome of a new botybirnavirus that we have named "Botrytis cinerea botybirnavirus 1".
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Affiliation(s)
- Luis Cottet
- Laboratorio de Control Biológico y Nanotecnología, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Chile, Alameda 3363, 9170022, Estación Central, Santiago, Chile
| | - Christiaan A Potgieter
- Department of Biochemistry, Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa.,Deltamune (Pty) Ltd, Lyttelton, Centurion, South Africa
| | - Miguel E Castro
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Avenida Ejército Libertador 146, Santiago, Chile
| | - Antonio Castillo
- Laboratorio de Control Biológico y Nanotecnología, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Chile, Alameda 3363, 9170022, Estación Central, Santiago, Chile.
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25
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Ma G, Liang Z, Hua H, Zhou T, Wu X. Complete genome sequence of a new botybirnavirus isolated from a phytopathogenic Alternaria alternata in China. Arch Virol 2019; 164:1225-1228. [DOI: 10.1007/s00705-019-04189-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 01/14/2019] [Indexed: 11/29/2022]
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26
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Wang H, Li C, Cai L, Fang S, Zheng L, Yan F, Zhang S, Liu Y. The complete genomic sequence of a novel botybirnavirus isolated from a phytopathogenic Bipolaris maydis. Virus Genes 2018; 54:733-736. [PMID: 29967958 DOI: 10.1007/s11262-018-1584-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/26/2018] [Indexed: 01/22/2023]
Abstract
Bipolaris maydis is the causal agent of corn southern leaf blight. Here, we report a novel double-stranded RNA (dsRNA) mycovirus designated Bipolaris maydis botybirnavirus 1 (BmBRV1) from B. maydis strain JZ11 in Jingzhou, Hubei province of China. BmBRV1 has a genome consisting of two dsRNAs (dsRNA1 and dsRNA2) with a size of 6435 and 5987 bp, respectively, each of which contains a single open reading frame (ORF). The two polyproteins encoded by dsRNA1 and dsRNA2 share the highest amino acid identities of 81.8 and 75.3%, respectively, with the RdRp and coat protein of Sclerotinia sclerotiorum botybirnavirus 1 (SsBRV1), a tentative species of the genus Botybirnavirus. Phylogenetic analysis based on the amino acid sequences of RdRp indicated that BmBRV1 belongs to a distinct species of the newly proposed family Botybirnaviridae.
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Affiliation(s)
- Haoran Wang
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Cong Li
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China.,Hunan Plant Protection Institute, Changsha, 410125, Hunan, China.,Longping Branch, Graduate School of Hunan University, Changsha, 410125, Hunan, China
| | - Lina Cai
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Shouguo Fang
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Limin Zheng
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China.,Longping Branch, Graduate School of Hunan University, Changsha, 410125, Hunan, China
| | - Fei Yan
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Songbai Zhang
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yong Liu
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China. .,Longping Branch, Graduate School of Hunan University, Changsha, 410125, Hunan, China.
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27
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Mu F, Xie J, Cheng S, You MP, Barbetti MJ, Jia J, Wang Q, Cheng J, Fu Y, Chen T, Jiang D. Virome Characterization of a Collection of S. sclerotiorum from Australia. Front Microbiol 2018; 8:2540. [PMID: 29375495 PMCID: PMC5768646 DOI: 10.3389/fmicb.2017.02540] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/06/2017] [Indexed: 11/13/2022] Open
Abstract
Sclerotinia sclerotiorum is a devastating plant pathogen that attacks numerous economically important broad acre and vegetable crops worldwide. Mycoviruses are widespread viruses that infect fungi, including S. sclerotiorum. As there were no previous reports of the presence of mycoviruses in this pathogen in Australia, studies were undertaken using RNA_Seq analysis to determine the diversity of mycoviruses in 84 Australian S. sclerotiorum isolates collected from various hosts. After RNA sequences were subjected to BLASTp analysis using NCBI database, 285 contigs representing partial or complete genomes of 57 mycoviruses were obtained, and 34 of these (59.6%) were novel viruses. These 57 viruses were grouped into 10 distinct lineages, namely Endornaviridae (four novel mycoviruses), Genomoviridae (isolate of SsHADV-1), Hypoviridae (two novel mycoviruses), Mononegavirales (four novel mycovirusess), Narnaviridae (10 novel mycoviruses), Partitiviridae (two novel mycoviruses), Ourmiavirus (two novel mycovirus), Tombusviridae (two novel mycoviruses), Totiviridae (one novel mycovirus), Tymovirales (five novel mycoviruses), and two non-classified mycoviruses lineages (one Botrytis porri RNA virus 1, one distantly related to Aspergillus fumigatus tetramycovirus-1). Twenty-five mitoviruses were determined and mitoviruses were dominant in the isolates tested. This is not only the first study to show existence of mycoviruses in S. sclerotiorum in Australia, but highlights how they are widespread and that many novel mycoviruses occur there. Further characterization of these mycoviruses is warranted, both in terms of exploring these novel mycoviruses for innovative biocontrol of Sclerotinia diseases and in enhancing our overall knowledge on viral diversity, taxonomy, ecology, and evolution.
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Affiliation(s)
- Fan Mu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shufen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Ming Pei You
- Faculty of Science, UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Martin J. Barbetti
- Faculty of Science, UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
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28
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Abstract
Plant-associated fungi are infected by viruses at the incidence rates from a few % to over 90%. Multiple viruses often coinfect fungal hosts, and occasionally alter their phenotypes, but most of the infections are asymptomatic. Phenotypic alterations are grouped into two types: harmful or beneficial to the host fungi. Harmful interactions between viruses and hosts include hypovirulence and/or debilitation that are documented in a number of phytopathogenic fungi, exemplified by the chestnut blight, white root rot, and rapeseed rot fungi. Beneficial interactions are observed in a limited number of plant endophytic and pathogenic fungi where heat tolerance and virulence are enhanced, respectively. Coinfections of fungi provided a platform for discoveries of interesting virus/virus interactions that include synergistic, as in the case for those in plants, and unique antagonistic and mutualistic interactions between unrelated RNA viruses. Also discussed here are coinfection-induced genome rearrangements and frequently observed coinfections by the simplest positive-strand RNA virus, the mitoviruses.
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Affiliation(s)
- Bradley I Hillman
- Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, United States.
| | - Aulia Annisa
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan.
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29
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Characterization of a novel botybirnavirus isolated from a phytopathogenic Alternaria fungus. Arch Virol 2017; 162:3907-3911. [DOI: 10.1007/s00705-017-3543-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/07/2017] [Indexed: 10/18/2022]
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