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Battersby JL, Stevens DA, Coutts RHA, Havlíček V, Hsu JL, Sass G, Kotta-Loizou I. The Expanding Mycovirome of Aspergilli. J Fungi (Basel) 2024; 10:585. [PMID: 39194910 DOI: 10.3390/jof10080585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024] Open
Abstract
Mycoviruses are viruses that infect fungi and are widespread across all major fungal taxa, exhibiting great biological diversity. Since their discovery in the 1960s, researchers have observed a myriad of fungal phenotypes altered due to mycoviral infection. In this review, we examine the nuanced world of mycoviruses in the context of the medically and agriculturally important fungal genus, Aspergillus. The advent of RNA sequencing has revealed a previous underestimate of viral prevalence in fungi, in particular linear single-stranded RNA viruses, and here we outline the diverse viral families known to date that contain mycoviruses infecting Aspergillus. Furthermore, we describe these novel mycoviruses, highlighting those with peculiar genome structures, such as a split RNA dependent RNA polymerase gene. Next, we delineate notable mycovirus-mediated phenotypes in Aspergillus, in particular reporting on observations of mycoviruses that affect their fungal host's virulence and explore how this may relate to virus-mediated decreased stress tolerance. Furthermore, mycovirus effects on microbial competition and antifungal resistance are discussed. The factors that influence the manifestation of these phenotypes, such as temperature, fungal life stage, and infection with multiple viruses, among others, are also evaluated. In addition, we attempt to elucidate the molecular mechanisms that underpin these phenotypes, examining how mycoviruses can be targets, triggers, and even suppressors of RNA silencing and how this can affect fungal gene expression and phenotypes. Finally, we highlight the potential therapeutic applications of mycoviruses and how, in an approach analogous to bacteriophage therapy, their ability to produce hypovirulence in Aspergillus might be used to attenuate invasive aspergillosis infections in humans.
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Affiliation(s)
- Josephine L Battersby
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Department of Clinical, Pharmaceutical and Biological Science, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - David A Stevens
- California Institute for Medical Research, San Jose, CA 95128, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert H A Coutts
- Department of Clinical, Pharmaceutical and Biological Science, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Vladimír Havlíček
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic
- Department of Analytical Chemistry, Palacky University, 17. Listopadu 2, 779 00 Olomouc, Czech Republic
| | - Joe L Hsu
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gabriele Sass
- California Institute for Medical Research, San Jose, CA 95128, USA
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Department of Clinical, Pharmaceutical and Biological Science, University of Hertfordshire, Hatfield AL10 9AB, UK
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Hua H, Zhang X, Liu L, Wu X. A Novel Strain of Fusarium oxysporum Alternavirus 1 Isolated from Fusarium oxysporum f. sp. melonis Strain T-BJ17 Confers Hypovirulence and Increases the Sensitivity of Its Host Fungus to Difenoconazole and Pydiflumetofen. Viruses 2024; 16:901. [PMID: 38932193 PMCID: PMC11209391 DOI: 10.3390/v16060901] [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: 03/17/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
In the current study, a novel strain of Fusarium oxysporum alternavirus 1 (FoAV1) was identified from the Fusarium oxysporum f. sp. melonis (FOM) strain T-BJ17 and was designated as Fusarium oxysporum alternavirus 1-FOM (FoAV1-FOM). Its genome consists of four dsRNA segments of 3515 bp (dsRNA1), 2663 bp (dsRNA2), 2368 bp (dsRNA3), and 1776 bp (dsRNA4) in length. Open reading frame 1 (ORF1) in dsRNA1 was found to encode a putative RNA-dependent RNA polymerase (RdRp), whose amino acid sequence was 99.02% identical to that of its counterpart in FoAV1; while ORF2 in dsRNA2, ORF3 in dsRNA3, and ORF4 in dsRNA4 were all found to encode hypothetical proteins. Strain T-BJ17-VF, which was verified to FoAV1-FOM-free, was obtained using single-hyphal-tip culture combined with high-temperature treatment to eliminate FoAV1-FOM from strain T-BJ17. The colony growth rate, ability to produce spores, and virulence of strain T-BJ17 were significantly lower than those of T-BJ17-VF, while the dry weight of the mycelial biomass and the sensitivity to difenoconazole and pydiflumetofen of strain T-BJ17 were greater than those of T-BJ17-VF. FoAV1-FOM was capable of 100% vertical transmission via spores. To our knowledge, this is the first time that an alternavirus has infected FOM, and this is the first report of hypovirulence and increased sensitivity to difenoconazole and pydiflumetofen induced by FoAV1-FOM infection in FOM.
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Affiliation(s)
| | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China (X.Z.); (L.L.)
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3
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Xu X, Li J, Hai D, Wang Y, Li J, Zha Y. Complete genome sequence of a novel alternavirus isolated from the phytopathogenic fungus Colletotrichum fioriniae. Arch Virol 2024; 169:79. [PMID: 38519762 DOI: 10.1007/s00705-024-06010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/04/2024] [Indexed: 03/25/2024]
Abstract
A novel double-strand RNA (dsRNA) mycovirus, named "Colletotrichum fioriniae alternavirus1" (CfAV1), was isolated from the strain CX7 of Colletotrichum fioriniae, the causal agent of walnut anthracnose. The complete genome of CfAV1 is composed of three dsRNA segments: dsRNA1 (3528 bp), dsRNA2 (2485 bp), and dsRNA3 (2481 bp). The RNA-dependent RNA polymerase (RdRp) is encoded by dsRNA1, while both dsRNA2 and dsRNA3 encode hypothetical proteins. Based on multiple sequence alignments and phylogenetic analysis, CfAV1 is identified as a new member of the family Alternaviridae. This is the first report of an alternavirus that infects the phytopathogenic fungus C. fioriniae.
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Affiliation(s)
- Xiaowen Xu
- Hubei Academy of Forestry, Wuhan, 430074, Hubei Province, People's Republic of China.
| | - Jincang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Du Hai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Yixun Wang
- Hubei Academy of Forestry, Wuhan, 430074, Hubei Province, People's Republic of China
| | - Jinying Li
- Hubei Academy of Forestry, Wuhan, 430074, Hubei Province, People's Republic of China
| | - Yuping Zha
- Hubei Academy of Forestry, Wuhan, 430074, Hubei Province, People's Republic of China.
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4
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Liu F, Xia L, Cao S, Sun H, Chen H, Deng Q, Li W. A novel alternavirus with three dsRNA segments from Fusarium pseudograminearum, the pathogen of Fusarium crown rot in wheat. Arch Virol 2024; 169:49. [PMID: 38366289 DOI: 10.1007/s00705-024-05982-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/26/2023] [Indexed: 02/18/2024]
Abstract
Three dsRNA segments were detected in Fusarium pseudograminearum strain CF14029, a pathogen causing Fusarium crown rot in China. Characterization and sequence analysis confirmed that these dsRNA sequences originated from the same virus. The viral genome consists of three dsRNA segments: dsRNA1 (3,560 nt in length), encoding an RNA-dependent RNA polymerase (RdRp), dsRNA2 (2,544 nt in length), encoding a hypothetical protein, and dsRNA3 (2,478 nt in length), encoding a putative coat protein (CP). Phylogenetic analysis based on the RdRp and CP amino acid sequences revealed a high degree of similarity of this virus to members of the genus Alternavirus, family Alternaviridae, isolated from other Fusarium fungi. As a novel member of the genus Alternavirus, this virus was provisionally named "Fusarium pseudograminearum alternavirus 1" (FpgAV1). Like other alternaviruses found in Fusarium species, the positive-sense strand of each genomic dsRNA of FpgAV1 possesses a poly(A) tail and a distinctive 5'-terminal octamer sequence (5'-GCT GTG TG-3'). This is the first report of the genomic sequence of an alternavirus identified in F. pseudograminearum.
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Affiliation(s)
- Fuyu Liu
- College of Agriculture, Yangtze University, 434025, Hubei, Jingzhou, China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, Jiangsu, China
| | - Lele Xia
- College of Plant Protection, Nanjing Agricultural University, 210095, Jiangsu, Nanjing, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, Jiangsu, China
| | - Haiyan Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, Jiangsu, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, Jiangsu, China
| | - Qingchao Deng
- College of Agriculture, Yangtze University, 434025, Hubei, Jingzhou, China.
| | - Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, Jiangsu, China.
- College of Plant Protection, Nanjing Agricultural University, 210095, Jiangsu, Nanjing, China.
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5
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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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6
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Pielhop TP, Popp C, Fricke S, Knierim D, Margaria P, Maiß E. Molecular characterization of two new alternaviruses identified in members of the fungal family Nectriaceae. Arch Microbiol 2023; 205:129. [PMID: 36947239 PMCID: PMC10033562 DOI: 10.1007/s00203-023-03477-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/23/2023]
Abstract
Since the first report in 2009, at least ten additional viruses have been identified and assigned to the proposed virus family Alternaviridae. Here we report two new mycoviruses tentatively assigned to this family, both identified as members of the fungal family Nectriaceae, which were isolated from surface-disinfected apple roots (Malus x domestica, Borkh.) affected by apple replant disease (ARD). ARD is a highly complex, worldwide-occurring disease resulting from plant reactions to a disturbed (micro)-biome and leads to high economic losses every year. The first alternavirus characterized in this study was identified in a Dactylonectria torresensis isolate. The virus was tentatively named dactylonectria torresensis alternavirus 1 (DtAV1) as the first member of the proposed new species Alternavirus dactylonectriae. The second virus was identified in an isolate of Ilyonectria robusta and was tentatively named ilyonectria robusta alternavirus 1 (IrAV1) as the first member of the proposed new species Alternavirus ilyonectriae. Full genomic sequences of the viruses were determined and are presented. Further, we found hints for putative components of a methyl transferase machinery using in silico approaches. This putative protein domain is encoded by segment 2. However, this result only establishes the basis for subsequent studies in which the function must be confirmed experimentally in vitro. Thus, this is the first study where a function is predicted to all three genomic segments within the group of the alternaviruses. These findings provide further insights into the virome of ARD-associated fungi and are therefore another brick in the wall of understanding the complexity of the disease.
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Affiliation(s)
- Tom P Pielhop
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Carolin Popp
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Sebastian Fricke
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Dennis Knierim
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124, Braunschweig, Germany
| | - Paolo Margaria
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124, Braunschweig, Germany
| | - Edgar Maiß
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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7
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Zhang X, Wu C, Hua H, Cai Q, Wu X. Characterization of the First Alternavirus Identified in Fusarium avenaceum, the Causal Agent of Potato Dry Rot. Viruses 2023; 15:145. [PMID: 36680185 PMCID: PMC9864086 DOI: 10.3390/v15010145] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
A novel virus with a double-stranded RNA (dsRNA) genome was isolated from Fusarium avenaceum strain GS-WW-224, the causal agent of potato dry rot. The virus has been designated as Fusarium avenaceum alternavirus 1 (FaAV1). Its genome consists of two dsRNA segments, 3538 bp (dsRNA1) and 2477 bp (dsRNA2) in length, encoding RNA-dependent RNA polymerase (RdRp) and a hypothetical protein (HP), respectively. The virions of FaAV1 are isometric spherical and approximately 30 nm in diameter. Multiple sequence alignments and phylogenetic analyses based on the amino acid sequences of RdRp and HP indicated that FaAV1 appears to be a new member of the proposed family Alternaviridae. No significant differences in colony morphology and spore production were observed between strains GS-WW-224 and GS-WW-224-VF, the latter strain being one in which FaAV1 was eliminated from strain GS-WW-224. Notably, however, the dry weight of mycelial biomass of GS-WW-224 was higher than that of mycelial biomass of GS-WW-224-VF. The depth and the width of lesions on potato tubers caused by GS-WW-224 were significantly greater, relative to GS-WW-224-VF, suggesting that FaAV1 confers hypervirulence to its host, F. avenaceum. Moreover, FaAV1 was successfully transmitted horizontally from GS-WW-224 to ten other species of Fusarium, and purified virions of FaAV1 were capable of transfecting wounded hyphae of the ten species of Fusarium. This is the first report of an alternavirus infecting F. avenaceum and conferring hypervirulence.
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Affiliation(s)
| | | | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China
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8
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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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Lutz T, Langer G, Heinze C. Complete genome sequence of a novel alternavirus infecting the fungus Ilyonectria crassa. Arch Virol 2023; 168:34. [PMID: 36609790 PMCID: PMC9825354 DOI: 10.1007/s00705-022-05652-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/30/2022] [Indexed: 01/09/2023]
Abstract
A novel dsRNA mycovirus named Ilyonectria crassa alternavirus 1 (IcAV1) was found in Ilyonectria crassa isolate NW-FVA 1829. The fungus was isolated from an ash (Fraxinus excelsior L.) necrotic trunk disc infected with Hymenoscyphus fraxineus [(T. Kowalski) Baral, Queloz, Hosoya] causing ash dieback. The complete genome of IcAV1 is composed of three segments, each containing a single ORF on the positive-sense RNA. The extreme 5' UTRs of dsRNA 1 (3604 bp), dsRNA 2 (2547 bp), and dsRNA 3 (2518 bp) share a conserved hexadecamer sequence (5'-GGCTGTGTGTTTAGTT-3') and are capped. The 3' UTRs are polyadenylated. In silico analysis showed that the viral RdRP is encoded on dsRNA 1 and the capsid-protein subunits are encoded on dsRNA 3. Maximum-likelihood analysis of the aa sequence of the viral RdRP showed that IcAV1 clusters with alternaviruses from Fusarium spp., while the type member of the proposed family "Alternaviridae", Alternaria alternata virus 1 (AaV1), formed a clade together with Stemphylium lycopersici mycovirus (SlV). The function of the protein encoded on segment 2 is unknown. Based on its genome organization and its phylogenetic position, IcAV1 is suggested to be a new member of the proposed family "Alternaviridae". This is the first report of a mycovirus infecting I. crassa.
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Affiliation(s)
- Tobias Lutz
- Institute of Plant Science and Microbiology, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Gitta Langer
- Nordwestdeutsche Forstliche Versuchsanstalt, Grätzelstr. 2, 37079, Göttingen, Germany
| | - Cornelia Heinze
- Institute of Plant Science and Microbiology, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
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Characterization of a novel alternavirus infecting the fungal pathogen Fusarium solani. Virus Res 2022; 317:198817. [DOI: 10.1016/j.virusres.2022.198817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022]
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Zhang Y, Shi N, Wang P, Zhu Q, Yang G, Huang B. Molecular characterization of a novel alternavirus infecting the entomopathogenic fungus Cordyceps chanhua. Arch Virol 2022; 167:1467-1470. [PMID: 35412147 DOI: 10.1007/s00705-022-05446-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/08/2022] [Indexed: 11/24/2022]
Abstract
In this study, a novel double-stranded (ds) RNA mycovirus, named Cordyceps chanhua alternavirus 1 (CcAV1), was detected in the entomogenous fungus Cordyceps chanhua in China and characterized. The complete genome of CcAV1 is composed of three dsRNA segments: dsRNA 1 (3,512 bp), dsRNA 2 (2,655 bp), and dsRNA 3 (2,415 bp). Each of the three dsRNAs possesses a single open reading frame (ORF). dsRNA 1 encodes a putative RNA-dependent RNA polymerase (RdRp), and dsRNA 2 and dsRNA 3 encode hypothetical protein 1 (HP 1) and hypothetical protein 2 (HP 2), respectively. The predicted amino acid sequences of the putative RdRp, HP 1, and HP 2 had the highest identity of 66.99%, 49.30%, and 56.91%, respectively, to those of Aspergillus foetidus dsRNA mycovirus. A maximum-likelihood phylogenetic tree based on RdRp amino acid sequences showed that CcAV1 clustered with members of the proposed family "Alternaviridae". Hence, we propose that Cordyceps chanhua alternavirus 1 is a novel member of the proposed family "Alternaviridae".
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Affiliation(s)
- Yuxiang Zhang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Najie Shi
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China
| | - Ping Wang
- 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
- School of Plant Protection, 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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Molecular Characterization of the First Alternavirus Identified in Fusarium oxysporum. Viruses 2021; 13:v13102026. [PMID: 34696456 PMCID: PMC8538667 DOI: 10.3390/v13102026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 01/25/2023] Open
Abstract
A novel mycovirus named Fusarium oxysporum alternavirus 1(FoAV1) was identified as infecting Fusarium oxysporum strain BH19, which was isolated from a fusarium wilt diseased stem of Lilium brownii. The genome of FoAV1 contains four double-stranded RNA (dsRNA) segments (dsRNA1, dsRNA 2, dsRNA 3 and dsRNA 4, with lengths of 3.3, 2.6, 2.3 and 1.8 kbp, respectively). Additionally, dsRNA1 encodes RNA-dependent RNA polymerase (RdRp), and dsRNA2- dsRNA3- and dsRNA4-encoded hypothetical proteins (ORF2, ORF3 and ORF4), respectively. A homology BLAST search, along with multiple alignments based on RdRp, ORF2 and ORF3 sequences, identified FoAV1 as a novel member of the proposed family "Alternaviridae". Evolutionary relation analyses indicated that FoAV1 may be related to alternaviruses, thus dividing the family "Alternaviridae" members into four clades. In addition, we determined that dsRNA4 was dispensable for replication and may be a satellite-like RNA of FoAV1-and could perhaps play a role in the evolution of alternaviruses. Our results provided evidence for potential genera establishment within the proposed family "Alternaviridae". Additionally, FoAV1 exhibited biological control of Fusarium wilt. Our results also laid the foundations for the further study of mycoviruses within the family "Alternaviridae", and provide a potential agent for the biocontrol of diseases caused by F. oxysporum.
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Quintanilha-Peixoto G, Fonseca PLC, Raya FT, Marone MP, Bortolini DE, Mieczkowski P, Olmo RP, Carazzolle MF, Voigt CA, Soares ACF, Pereira GAG, Góes-Neto A, Aguiar ERGR. The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses. Microorganisms 2021; 9:microorganisms9081704. [PMID: 34442783 PMCID: PMC8400513 DOI: 10.3390/microorganisms9081704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/29/2022] Open
Abstract
Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.
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Affiliation(s)
- Gabriel Quintanilha-Peixoto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Paula Luize Camargos Fonseca
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Fábio Trigo Raya
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Marina Pupke Marone
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Dener Eduardo Bortolini
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA;
| | - Roenick Proveti Olmo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- CNRS UPR9022, INSERM U1257, Université de Strasbourg, 67084 Strasbourg, France
| | - Marcelo Falsarella Carazzolle
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | | | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, Brazil;
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
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Molecular characterization of a novel totivirus infecting the basal fungus Conidiobolus heterosporus. Arch Virol 2021; 166:1801-1804. [PMID: 33866414 DOI: 10.1007/s00705-021-05054-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/09/2021] [Indexed: 10/21/2022]
Abstract
Mycoviruses are widely distributed in fungi, but only a few mycoviruses have been reported in basal fungi to date. Here, we characterized a novel totivirus isolated from the basal fungus Conidiobolus heterosporus, and we designated this virus as "Conidiobolus heterosporus totivirus 1" (ChTV1). The complete genome of ChTV1 contains two discontinuous open reading frames (ORFs), ORF1 and ORF2, encoding a putative coat protein (CP) and a putative RNA-dependent RNA polymerase (RdRP), respectively. Phylogenetic analysis based on RdRP sequences showed that ChTV1 clustered with members of the genus Totivirus. The RdRP of ChTV1 has 51% sequence identity to that of Trichoderma koningiopsis totivirus 1 (TkTV1), which is the highest among mycoviruses. However, TkTV1 formed a distinct cluster with Wuhan insect virus 27, with 63% RdRP sequence identity, although Wuhan insect virus 27 has not been described, and its host represents a different kingdom. Therefore, we propose that ChTV1 is a new member of the genus Totivirus, family Totiviridae.
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15
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Nazik H, Kotta-Loizou I, Sass G, Coutts RHA, Stevens DA. Virus Infection of Aspergillus fumigatus Compromises the Fungus in Intermicrobial Competition. Viruses 2021; 13:v13040686. [PMID: 33923408 PMCID: PMC8073786 DOI: 10.3390/v13040686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Aspergillus and Pseudomonas compete in nature, and are the commonest bacterial and fungal pathogens in some clinical settings, such as the cystic fibrosis lung. Virus infections of fungi occur naturally. Effects on fungal physiology need delineation. A common reference Aspergillus fumigatus strain, long studied in two (of many) laboratories, was found infected with the AfuPmV-1 virus. One isolate was cured of virus, producing a virus-free strain. Virus from the infected strain was purified and used to re-infect three subcultures of the virus-free fungus, producing six fungal strains, otherwise isogenic. They were studied in intermicrobial competition with Pseudomonasaeruginosa. Pseudomonas culture filtrates inhibited forming or preformed Aspergillus biofilm from infected strains to a greater extent, also seen when Pseudomonas volatiles were assayed on Aspergillus. Purified iron-chelating Pseudomonas molecules, known inhibitors of Aspergillus biofilm, reproduced these differences. Iron, a stimulus of Aspergillus, enhanced the virus-free fungus, compared to infected. All infected fungal strains behaved similarly in assays. We show an important consequence of virus infection, a weakening in intermicrobial competition. Viral infection may affect the outcome of bacterial–fungal competition in nature and patients. We suggest that this occurs via alteration in fungal stress responses, the mechanism best delineated here is a result of virus-induced altered Aspergillus iron metabolism.
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Affiliation(s)
- Hasan Nazik
- California Institute for Medical Research, 2260 Clove Dr., San Jose, CA 95128, USA; (H.N.); (G.S.)
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK;
| | - Gabriele Sass
- California Institute for Medical Research, 2260 Clove Dr., San Jose, CA 95128, USA; (H.N.); (G.S.)
| | - Robert H. A. Coutts
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK;
| | - David A. Stevens
- California Institute for Medical Research, 2260 Clove Dr., San Jose, CA 95128, USA; (H.N.); (G.S.)
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 95128, USA
- Correspondence: ; Tel.: +1-408-998-4554
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16
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Sutela S, Poimala A, Vainio EJ. Viruses of fungi and oomycetes in the soil environment. FEMS Microbiol Ecol 2019; 95:5542194. [DOI: 10.1093/femsec/fiz119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACTSoils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus–host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.
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Affiliation(s)
- Suvi Sutela
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Anna Poimala
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
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Gilbert KB, Holcomb EE, Allscheid RL, Carrington JC. Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes. PLoS One 2019; 14:e0219207. [PMID: 31339899 PMCID: PMC6655640 DOI: 10.1371/journal.pone.0219207] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/18/2019] [Indexed: 11/25/2022] Open
Abstract
The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
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Affiliation(s)
- Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Emily E. Holcomb
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Robyn L. Allscheid
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - James C. Carrington
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
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18
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Li P, Bhattacharjee P, Wang S, Zhang L, Ahmed I, Guo L. Mycoviruses in Fusarium Species: An Update. Front Cell Infect Microbiol 2019; 9:257. [PMID: 31380300 PMCID: PMC6657619 DOI: 10.3389/fcimb.2019.00257] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
Fusarium is an important genus of plant pathogenic fungi, and is widely distributed in soil and associated with plants worldwide. The diversity of mycoviruses in Fusarium is increasing continuously due to the development and extensive use of state-of-the-art RNA deep sequencing techniques. To date, fully-sequenced mycoviruses have been reported in 13 Fusarium species: Fusarium asiaticum, F. boothii, F. circinatum, F. coeruleum, F. globosum, F. graminearum, F. incarnatum, F. langsethiae, F. oxysporum, F. poae, F. pseudograminearum, F. solani, and F. virguliforme. Most Fusarium mycoviruses establish latent infections, but some mycoviruses such as Fusarium graminearum virus 1 (FgV1), Fusarium graminearum virus-ch9 (FgV-ch9), Fusarium graminearum hypovirus 2 (FgHV2), and Fusarium oxysporum f. sp. dianthi mycovirus 1 (FodV1) cause hypovirulence. Rapid advances in various omics technologies used to elucidate genes or biological processes can facilitate an improved understanding of mycovirus-host interactions. The review aims to illuminate the recent advances in studies of mycoviruses in Fusarium, including those related to diversity, molecular mechanisms of virus-host interaction. We also discuss the induction and suppression of RNA silencing including the role of RNAi components as an antiviral defense response.
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Affiliation(s)
- Pengfei Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pallab Bhattacharjee
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuangchao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Irfan Ahmed
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihua Guo
- 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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19
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van de Sande WWJ, Vonk AG. Mycovirus therapy for invasive pulmonary aspergillosis? Med Mycol 2019; 57:S179-S188. [PMID: 30816971 DOI: 10.1093/mmy/myy073] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/21/2018] [Indexed: 12/13/2022] Open
Abstract
With the current revived interest in the use of bacteriophages for the treatment of bacterial infections, the study of mycoviruses as novel therapeutic solutions for invasive aspergillosis is the logical next step. Although ssRNA, dsRNA, and ssDNA mycoviruses have been identified, the majority of characterised mycoviruses have dsRNA genomes. Prevalence of dsRNA mycoviruses in Aspergillus spp. varies, and mycoviruses can have different effects on their fungal hosts: hypovirulence, hypervirulence, or a killer phenotype. Therapeutically, extracellular transmission of the mycovirus is essential. DsRNA mycoviruses lack an extracellular phase; however, a single ssDNA mycovirus with homologues in Aspergillus genomes has been described with an extracellular mode of transmission. Mycoviruses can induce hypovirulence or a killer phenotype, and both can be exploited therapeutically. Mycoviruses inducing hypovirulence have been used to control chestnut blight, however for aspergillosis no such mycovirus has been identified yet. Mycovirus encoded killer toxins or anti-idiotypic antibodies and killer peptides derived from these have been demonstrated to control fungal infections including aspergillosis in animals. This indicates that mycoviruses inducing both phenotypes could be exploited therapeutically as long as the right mycovirus has been identified.
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Affiliation(s)
- Wendy W J van de Sande
- ErasmusMC, Department of Medical Microbiology and Infectious Diseases, Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
| | - Alieke G Vonk
- ErasmusMC, Department of Medical Microbiology and Infectious Diseases, Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
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20
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Zhang X, Xie Y, Zhang F, Sun H, Zhai Y, Zhang S, Yuan H, Zhou L, Gao F, Li H. Complete genome sequence of an alternavirus from the phytopathogenic fungus Fusarium incarnatum. Arch Virol 2019; 164:923-925. [DOI: 10.1007/s00705-018-04128-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/23/2018] [Indexed: 10/27/2022]
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Je M, Kim H, Son HS. Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. Virol J 2019; 16:10. [PMID: 30651145 PMCID: PMC6335760 DOI: 10.1186/s12985-019-1115-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/01/2019] [Indexed: 12/21/2022] Open
Abstract
Background Mycoviruses that infect fungi generally do not have a significant effect on the host and, instead, reduce the toxicity of the fungi. However, recent studies have shown that polymycovirus-1, a mycovirus that infects Aspergillus species known to cause disease in humans, is related to increased virulence of the fungus. Methods Comparative analysis was performed of RdRP gene codon usage patterns of Aspergillus fumigatus polymycovirus-1 (AfuPmV-1) and other mycoviruses known to infect Aspergillus spp. to examine the genetic characteristics of AfuPmV-1. In addition, codon usage analysis was performed to determine whether the nucleotide composition and codon usage characteristics of AfuPmV-1 were also present in other polymycoviruses and hypervirulence-related mycoviruses. Phylogenetic analysis was also performed to investigate their evolutionary relationship. Results Analysis of nucleotide composition indicated that AfuPmV-1 had the highest GC content among analyzed mycoviruses and relative synonymous codon usage analysis indicated that all of the codons preferred by AfuPmV-1 ended with C or G, while codons ending with A or U were not observed. Moreover, the effective number of codons, the codon adaptation index, and correspondence analysis showed that AfuPmV-1 had greater codon preference compared with other mycoviruses and that AfuPmV-1 had relatively high adaptability to humans and fungi. These results were generally similar among polymycoviruses. Conclusions The codon usage pattern of AfuPmV-1 differs from other mycoviruses that infect Aspergillus spp. This difference may be related to the hypervirulence effect of AfuPmV-1. Analysis of AfuPmV-1 codon usage patterns could contribute to the identification and prediction of virulence effects of mycoviruses with similar genetic characteristics.
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Affiliation(s)
- Mikyung Je
- SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.,Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Hayeon Kim
- Department of Biomedical Laboratory Science, Kyungdong University, 815 Gyeonhwon-ro, Munmak, Wonju, Gangwondo, 24695, Korea
| | - Hyeon S Son
- SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea. .,Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
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Shah UA, Kotta-Loizou I, Fitt BDL, Coutts RHA. Identification, Molecular Characterization, and Biology of a Novel Quadrivirus Infecting the Phytopathogenic Fungus Leptosphaeria biglobosa. Viruses 2018; 11:E9. [PMID: 30585188 PMCID: PMC6356713 DOI: 10.3390/v11010009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/20/2018] [Accepted: 12/22/2018] [Indexed: 01/18/2023] Open
Abstract
Here we report the molecular characterisation of a novel dsRNA virus isolated from the filamentous, plant pathogenic fungus Leptosphaeria biglobosa and known to cause significant alterations to fungal pigmentation and growth and to result in hypervirulence, as illustrated by comparisons between virus-infected and -cured isogenic fungal strains. The virus forms isometric particles approximately 40⁻45 nm in diameter and has a quadripartite dsRNA genome structure with size ranges of 4.9 to 4 kbp, each possessing a single ORF. Sequence analysis of the putative proteins encoded by dsRNAs 1⁻4, termed P1⁻P4, respectively, revealed modest similarities to the amino acid sequences of equivalent proteins predicted from the nucleotide sequences of known and suspected members of the family Quadriviridae and for that reason the virus was nominated Leptosphaeria biglobosa quadrivirus-1 (LbQV-1). Sequence and phylogenetic analysis using the P3 sequence, which encodes an RdRP, revealed that LbQV-1 was most closely related to known and suspected quadriviruses and monopartite totiviruses rather than other quadripartite mycoviruses including chrysoviruses and alternaviruses. Of the remaining encoded proteins, LbQV-1 P2 and P4 are structural proteins but the function of P1 is unknown. We propose that LbQV-1 is a novel member of the family Quadriviridae.
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Affiliation(s)
- Unnati A Shah
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
| | - Ioly Kotta-Loizou
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Bruce D L Fitt
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
| | - Robert H A Coutts
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
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Okada R, Ichinose S, Takeshita K, Urayama SI, Fukuhara T, Komatsu K, Arie T, Ishihara A, Egusa M, Kodama M, Moriyama H. Molecular characterization of a novel mycovirus in Alternaria alternata manifesting two-sided effects: Down-regulation of host growth and up-regulation of host plant pathogenicity. Virology 2018; 519:23-32. [PMID: 29631173 DOI: 10.1016/j.virol.2018.03.027] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/11/2018] [Accepted: 03/30/2018] [Indexed: 11/28/2022]
Abstract
A double-stranded RNA (dsRNA) mycovirus was detected in a strain of Alternaria alternata showing impaired growth phenotypes. The A. alternata strain is the Japanese pear pathotype, which produces a host-specific AK-toxin. Sequence analysis of the viral genome dsRNAs revealed that this mycovirus consists of five dsRNAs and is evolutionarily related to members of the family Chrysoviridae; the virus was named Alternaria alternata chrysovirus 1 (AaCV1). AaCV1-ORF2 protein accumulated in dsRNA-high-titer sub-isolates with severely impaired phenotypes; heterologous AaCV1-ORF2 overexpression in Saccharomyces cerevisiae caused growth inhibition. In contrast to this yeast growth inhibition phenomenon, the dsRNA-high-titer isolates displayed enhanced pathogenicity against Japanese pear plants, in accordance with a 13-fold increase in AK-toxin level in one such isolate. These findings indicated that AaCV1 is a novel mycovirus that exhibits two contrasting effects, impairing growth of the host fungus while rendering the host 'hypervirulent' to the plant.
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Affiliation(s)
- Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Shun Ichinose
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Kana Takeshita
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Syun-Ichi Urayama
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Atsushi Ishihara
- Laboratory of Natural Product, Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
| | - Mayumi Egusa
- Laboratory of Plant Pathology, Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
| | - Motoichiro Kodama
- Laboratory of Plant Pathology, Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan; Laboratory of Plant Pathology, The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, Tottori 680-8553, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan.
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Complete Genome Sequence of a Fusarium graminearum Double-Stranded RNA Virus in a Newly Proposed Family, Alternaviridae. GENOME ANNOUNCEMENTS 2018; 6:6/8/e00064-18. [PMID: 29472334 PMCID: PMC5824011 DOI: 10.1128/genomea.00064-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We describe here a double-stranded RNA mycovirus, termed Fusarium graminearum alternavirus 1 (FgAV1/AH11), from the isolate AH11 of the phytopathogenic fungus F. graminearum. Phylogenetic analysis showed that FgAV1/AH11 belongs to a newly proposed family, Alternaviridae. This is the first report of a mycovirus in the family Alternaviridae that infects F. graminearum.
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A neo-virus lifestyle exhibited by a (+)ssRNA virus hosted in an unrelated dsRNA virus: Taxonomic and evolutionary considerations. Virus Res 2018; 244:75-83. [DOI: 10.1016/j.virusres.2017.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/04/2017] [Accepted: 11/05/2017] [Indexed: 12/21/2022]
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Kotta-Loizou I, Coutts RHA. Mycoviruses in Aspergilli: A Comprehensive Review. Front Microbiol 2017; 8:1699. [PMID: 28932216 PMCID: PMC5592211 DOI: 10.3389/fmicb.2017.01699] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/23/2017] [Indexed: 12/31/2022] Open
Abstract
Fungi, similar to all species, are susceptible to viral infection. Aspergillus is arguably the most well studied fungal genus because of its medical, ecological and economical significance. Mycoviruses were initially detected in Aspergillus species almost 50 years ago and the field continues to be active today with ground-breaking discoveries. The aim of the present review is to cover the scientific progress in all aspects of mycovirology as exemplified by Aspergillus-focused research. Initially an overview of the population studies illustrating the presence of mycoviruses in numerous important Aspergillus species, such as A. niger, A. flavus, and A. fumigatus with be presented. Moreover the intricacies of mycovirus transmission, both inter- and intra-species, will be discussed together with the methodologies used to investigate viral dispersion in a laboratory setting. Subsequently, the genomic features of all molecularly characterized mycoviruses to date will be analyzed in depth. These include members of established viral families, such as Partitiviridae, Chrysoviridae and Totiviridae, but also more recent, novel discoveries that led to the proposal of new viral families, such as Polymycoviridae, Alternaviridae and, in the context of the present review, Exartaviridae. Finally, the major issue of phenotypic effects of mycoviral infection on the host is addressed, including aflatoxin production in A. flavus, together with growth and virulence in A. fumigatus. Although the molecular mechanisms behind these phenomena are yet to be elucidated, recent studies suggest that by implication, RNA silencing may be involved.
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Affiliation(s)
- Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College LondonLondon, United Kingdom
| | - Robert H A Coutts
- Department of Biological and Environmental Sciences, University of HertfordshireHatfield, United Kingdom
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Osaki H, Sasaki A, Nomiyama K, Tomioka K. Multiple virus infection in a single strain of Fusarium poae shown by deep sequencing. Virus Genes 2016; 52:835-847. [DOI: 10.1007/s11262-016-1379-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/08/2016] [Indexed: 01/22/2023]
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Komatsu K, Katayama Y, Omatsu T, Mizutani T, Fukuhara T, Kodama M, Arie T, Teraoka T, Moriyama H. Genome sequence of a novel victorivirus identified in the phytopathogenic fungus Alternaria arborescens. Arch Virol 2016; 161:1701-4. [PMID: 26923927 DOI: 10.1007/s00705-016-2796-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Strains of the phytopathogenic fungus Alternaria spp. have been found to contain a variety of double-stranded RNA (dsRNA) elements indicative of mycovirus infection. Here, we report the molecular characterization of a novel dsRNA mycovirus, Alternaria arborescens victorivirus 1 (AaVV1), from A. arborescens, the tomato pathotype of A. alternata. Using next-generation sequencing of dsRNA purified from an A. arborescens strain from the United States of America, we found that the AaVV1 genome is 5203 bp in length and contains two open reading frames (ORF1 and 2) that overlap at the tetranucleotide AUGA. Proteins encoded by ORF1 and ORF2 showed significant similarities to the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp), respectively, of dsRNA mycoviruses of the genus Victorivirus. Pairwise comparisons and phylogenetic analysis of the deduced amino acid sequences of both CP and RdRp indicated that AaVV1 is a member of a distinct species of the genus Victorivirus in the family Totiviridae.
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Affiliation(s)
- Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Motoichiro Kodama
- Laboratory of Plant Pathology, Faculty of Agriculture, Tottori University, 4-101, Koyama-Minami, Tottori, 680-8553, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Tohru Teraoka
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
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A novel mycovirus from Aspergillus fumigatus contains four unique dsRNAs as its genome and is infectious as dsRNA. Proc Natl Acad Sci U S A 2015; 112:9100-5. [PMID: 26139522 DOI: 10.1073/pnas.1419225112] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We report the discovery and characterization of a double-stranded RNA (dsRNA) mycovirus isolated from the human pathogenic fungus Aspergillus fumigatus, Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1), which reveals several unique features not found previously in positive-strand RNA viruses, including the fact that it represents the first dsRNA (to our knowledge) that is not only infectious as a purified entity but also as a naked dsRNA. The AfuTmV-1 genome consists of four capped dsRNAs, the largest of which encodes an RNA-dependent RNA polymerase (RdRP) containing a unique GDNQ motif normally characteristic of negative-strand RNA viruses. The third largest dsRNA encodes an S-adenosyl methionine-dependent methyltransferase capping enzyme and the smallest dsRNA a P-A-S-rich protein that apparently coats but does not encapsidate the viral genome as visualized by atomic force microscopy. A combination of a capping enzyme with a picorna-like RdRP in the AfuTmV-1 genome is a striking case of chimerism and the first example (to our knowledge) of such a phenomenon. AfuTmV-1 appears to be intermediate between dsRNA and positive-strand ssRNA viruses, as well as between encapsidated and capsidless RNA viruses.
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Genome sequence of a novel mycovirus of Rhizoctonia solani, a plant pathogenic fungus. Virus Genes 2015; 51:167-70. [PMID: 26116286 DOI: 10.1007/s11262-015-1219-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
Here we present the genome sequence of a novel dsRNA virus we designed as Rhizoctonia solani RNA virus HN008 (RsRV-HN008) from a filamentous fungus R. solani. Its genome (7596 nucleotides) contains two non-overlapping open reading frames (ORF1 and ORF2). ORF1 encoded a 128 kDa protein that showed no significant identity to any other virus sequence in the NCBI database. ORF2 encoded a protein with a molecular weight of 140 kDa and shared a low percentage of sequence identity to the RdRps of unclassified dsRNA viruses. Sequence analysis revealed that RsRV-HN008 may be a member of a novel unclassified family of mycoviruses.
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The complete nucleotide sequence and genomic organization of a novel victorivirus with two non-overlapping ORFs, identified in the plant-pathogenic fungus Phomopsis vexans. Arch Virol 2015; 160:1805-9. [DOI: 10.1007/s00705-015-2420-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
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Sequence determination of a satellite RNA isolated from Aspergillus foetidus. Arch Virol 2015; 160:883-5. [PMID: 25613164 DOI: 10.1007/s00705-015-2338-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/10/2015] [Indexed: 10/24/2022]
Abstract
Aspergillus foetidus virus (AfV) has at least two distinct particle types, designated as AfV-fast (F) and AfV-slow (S). AfV-S includes AfV-S1, a victorivirus; AfV-S2, an unclassified satellite RNA; and AfV-S3, a previously uncharacterized dsRNA element. Here, we describe the complete sequence of AfV-S3, which is a short non-coding RNA with no known homologs. AfV-S3 is predicted to form an extended secondary structure, shares a 5' terminus with AfV-S2, and is a satellite RNA possibly dependent on both AfV-S1 and AfV-S2. This work concludes the sequencing of the A. foetidus virome.
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Zhong J, Lei XH, Zhu JZ, Song G, Zhang YD, Chen Y, Gao BD. Detection and sequence analysis of two novel co-infecting double-strand RNA mycoviruses in Ustilaginoidea virens. Arch Virol 2014; 159:3063-70. [DOI: 10.1007/s00705-014-2144-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/31/2014] [Indexed: 11/28/2022]
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Houbraken J, de Vries RP, Samson RA. Modern taxonomy of biotechnologically important Aspergillus and Penicillium species. ADVANCES IN APPLIED MICROBIOLOGY 2014; 86:199-249. [PMID: 24377856 DOI: 10.1016/b978-0-12-800262-9.00004-4] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Taxonomy is a dynamic discipline and name changes of fungi with biotechnological, industrial, or medical importance are often difficult to understand for researchers in the applied field. Species belonging to the genera Aspergillus and Penicillium are commonly used or isolated, and inadequate taxonomy or uncertain nomenclature of these genera can therefore lead to tremendous confusion. Misidentification of strains used in biotechnology can be traced back to (1) recent changes in nomenclature, (2) new taxonomic insights, including description of new species, and/or (3) incorrect identifications. Changes in the recent published International Code of Nomenclature for Algae, Fungi and Plants will lead to numerous name changes of existing Aspergillus and Penicillium species and an overview of the current names of biotechnological important species is given. Furthermore, in (biotechnological) literature old and invalid names are still used, such as Aspergillus awamori, A. foetidus, A. kawachii, Talaromyces emersonii, Acremonium cellulolyticus, and Penicillium funiculosum. An overview of these and other species with their correct names is presented. Furthermore, the biotechnologically important species Talaromyces thermophilus is here combined in Thermomyces as Th. dupontii. The importance of Aspergillus, Penicillium, and related genera is also illustrated by the high number of undertaken genome sequencing projects. A number of these strains are incorrectly identified or atypical strains are selected for these projects. Recommendations for correct strain selection are given here. Phylogenetic analysis shows a close relationship between the genome-sequenced strains of Aspergillus, Penicillium, and Monascus. Talaromyces stipitatus and T. marneffei (syn. Penicillium marneffei) are closely related to Thermomyces lanuginosus and Th. dupontii (syn. Talaromyces thermophilus), and these species appear to be distantly related to Aspergillus and Penicillium. In the last part of this review, an overview of heterothallic reproduction in Aspergillus and Penicillium is given. The new insights in the taxonomy of Aspergillus, Penicillium, and related genera will help to interpret the results generated with comparative genomics studies or other studies dealing with evolution of, for example, enzymes, mating-type loci, virulence genes, and secondary metabolite biosynthetic gene clusters.
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Affiliation(s)
- Jos Houbraken
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.
| | | | - Robert A Samson
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
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Zhong J, Zhou Q, Lei XH, Chen D, Shang HH, Zhu HJ. The nucleotide sequence and genome organization of two victoriviruses from the rice false smut fungus Ustilaginoidea virens. Virus Genes 2014; 48:570-3. [DOI: 10.1007/s11262-014-1050-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/08/2014] [Indexed: 01/11/2023]
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Abstract
Most of reported fungal viruses (mycoviruses) have double-stranded RNA (dsRNA) genomes. This may reflect the simple, easy method for mycovirus hunting that entails detection of dsRNAs as a sign of viral infections. There are an increasing number of screens of various fungi, particularly phytopathogenic fungi for viruses pathogenic to host fungi or able to confer hypovirulence to them. This bases on an attractive research field of biological control of fungal plant diseases using viruses (virocontrol), mainly targeting important phytopathogenic fungi. While isolated viruses usually induce asymptomatic symptoms, they show a considerably high level of diversity. As of 2014, fungal dsRNA viruses are classified into six families: Reoviridae, Totiviridae, Chrysoviridae, Partitiviridae, Megabirnaviridae and Quadriviridae. These exclude unassigned mycoviruses which will definitely be placed into distinct families and/or genera. In this review article, dsRNA viruses isolated from the kingdom Fungi including as-yet-unclassified taxa are overviewed. Some recent achievements in the related field are briefly introduced as well.
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Kozlakidis Z, Herrero N, Ozkan S, Bhatti MF, Coutts RHA. A novel dsRNA element isolated from the Aspergillus foetidus mycovirus complex. Arch Virol 2013; 158:2625-8. [PMID: 23827976 DOI: 10.1007/s00705-013-1779-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 01/22/2013] [Indexed: 10/26/2022]
Abstract
Aspergillus foetidus virus (AfV) contains at least two icosahedral particle types named AfV-fast (-F) and AfV-slow (-S), based on relative electrophoretic mobility. AfV-F is a quadripartite double-stranded RNA (dsRNA) virus, and AfV-S contains AfV-S1, which is a member of the genus Victorivirus in the family Totiviridae, and AfV-S2, which may be a satellite RNA or satellite virus and is described here. Analysis of the complete AfV-S2 nucleotide sequence reveals it to be significantly similar to an unclassified RNA from the fungus Rosellinia necatrix and distantly related to the RNA-dependent RNA polymerases of several single-stranded RNA genomes.
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Affiliation(s)
- Zisis Kozlakidis
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London, SW7 2AZ, UK
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Kozlakidis Z, Herrero N, Coutts RHA. The complete nucleotide sequence of a totivirus from Aspergillus foetidus. Arch Virol 2012; 158:263-6. [DOI: 10.1007/s00705-012-1368-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/28/2012] [Indexed: 10/28/2022]
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