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Santos JPN, Rodrigues GVP, Ferreira LYM, Monteiro GP, Fonseca PLC, Lopes ÍS, Florêncio BS, da Silva Junior AB, Ambrósio PE, Pirovani CP, Aguiar ERGR. The Virome of Cocoa Fermentation-Associated Microorganisms. Viruses 2024; 16:1226. [PMID: 39205200 PMCID: PMC11359646 DOI: 10.3390/v16081226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.
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Affiliation(s)
- João Pedro Nunes Santos
- Department of Health Sciences, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil;
| | - Gabriel Victor Pina Rodrigues
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (G.V.P.R.); (L.Y.M.F.); (C.P.P.)
| | - Lucas Yago Melo Ferreira
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (G.V.P.R.); (L.Y.M.F.); (C.P.P.)
| | - Gabriel Pereira Monteiro
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (G.V.P.R.); (L.Y.M.F.); (C.P.P.)
| | - Paula Luize Camargo Fonseca
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (G.V.P.R.); (L.Y.M.F.); (C.P.P.)
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Ícaro Santos Lopes
- Department of Genetics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Brenno Santos Florêncio
- Department of Engineering and Computing, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (B.S.F.); (A.B.d.S.J.); (P.E.A.)
| | - Aijalon Brito da Silva Junior
- Department of Engineering and Computing, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (B.S.F.); (A.B.d.S.J.); (P.E.A.)
| | - Paulo Eduardo Ambrósio
- Department of Engineering and Computing, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (B.S.F.); (A.B.d.S.J.); (P.E.A.)
| | - Carlos Priminho Pirovani
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (G.V.P.R.); (L.Y.M.F.); (C.P.P.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Engineering and Computing, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (B.S.F.); (A.B.d.S.J.); (P.E.A.)
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Ruiz-Padilla A, Rodríguez-Romero JL, Pacifico D, Chiapello M, Ayllón MA. Determination of the Mycovirome of a Necrotrophic Fungus. Methods Mol Biol 2024; 2732:83-101. [PMID: 38060119 DOI: 10.1007/978-1-0716-3515-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Next-generation sequencing (NGS) of total RNA has allowed the detection of novel viruses infecting different hosts, such as fungi, increasing our knowledge on virus horizontal transfer events among different hosts, virus diversity, and virus evolution. Here, we describe the detailed protocols for the isolation of the plant pathogenic fungus Botrytis cinerea, from grapevine plants showing symptoms of the mold gray disease, the culture and maintenance of the isolated B. cinerea strains, the extraction of total RNA from B. cinerea strains for NGS, the bioinformatics pipeline designed and followed to detect mycoviruses in the sequenced samples, and the validation of the in silico detected mycoviruses by different approaches.
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Affiliation(s)
- Ana Ruiz-Padilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Julio L Rodríguez-Romero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Davide Pacifico
- Institute of Bioscience and Bioresources, National Research Council of Italy, Palermo, Italy
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
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Li S, Ma Z, Zhang X, Cai Y, Han C, Wu X. Sixteen Novel Mycoviruses Containing Positive Single-Stranded RNA, Double-Stranded RNA, and Negative Single-Stranded RNA Genomes Co-Infect a Single Strain of Rhizoctonia zeae. J Fungi (Basel) 2023; 10:30. [PMID: 38248940 PMCID: PMC10817634 DOI: 10.3390/jof10010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
In the present study, sixteen novel RNA mycoviruses co-infecting a single strain of Rhizoctonia zeae (strain D40) were identified and molecularly characterized using metatranscriptome sequencing combined with a method for rapid amplification of cDNA ends. The fungal strain was isolated from diseased seedlings of sugar beet with damping-off symptoms. Based on genome analysis and phylogenetic analysis of amino acid sequences of RNA-dependent RNA polymerase, the sixteen mycoviruses associated with strain D40 contained three genome types with nine distinct lineages, including positive single-stranded RNA (Hypoviridae, Yadokariviridae, Botourmiaviridae, and Gammaflexiviridae), double-stranded RNA (Phlegiviridae, Megabirnaviridae, Megatotiviridae, and Yadonushiviridae), and negative single-stranded RNA (Tulasviridae), suggesting a complex composition of a mycoviral community in this single strain of R. zeae (strain D40). Full genome sequences of six novel mycoviruses and the nearly full-length sequences of the remaining ten novel mycoviruses were obtained. Furthermore, seven of these sixteen mycoviruses were confirmed to assemble virus particles present in the R. zeae strain D40. To the best of our knowledge, this is the first detailed study of mycoviruses infecting R. zeae.
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Affiliation(s)
| | | | | | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China; (S.L.); (Z.M.); (X.Z.); (Y.C.); (C.H.)
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Serafino G, Di Gianvito P, Giacosa S, Škrab D, Cocolin L, Englezos V, Rantsiou K. Survey of the yeast ecology of dehydrated grapes and strain selection for wine fermentation. Food Res Int 2023; 170:113005. [PMID: 37316074 DOI: 10.1016/j.foodres.2023.113005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
In this study we investigated the yeast population present on partially dehydrated Nebbiolo grapes destined for 'Sforzato di Valtellina', with the aim to select indigenous starters suitable for the production of this wine. Yeasts were enumerated, isolated, and identified by molecular methods (5.8S-ITS-RFLP and D1/D2 domain sequencing). A genetic, physiological (ethanol and sulphur dioxide tolerance, potentially useful enzymatic activities, hydrogen sulphide production, adhesive properties, and killer activity) and oenological (laboratory pure micro-fermentations) characterization was also carried out. Based on relevant physiological features, seven non-Saccharomyces strains were chosen for laboratory-scale fermentations, either in pure or in mixed-culture (simultaneous and sequential inoculum) with a commercial Saccharomyces cerevisiae strain. Finally, the best couples and inoculation strategy were further tested in mixed fermentations in winery. In both laboratory and winery, microbiological and chemical analyses were conducted during fermentation. The most abundant species on grapes were Hanseniaspora uvarum (27.4 % of the isolates), followed by Metschnikowia spp. (21.0 %) and Starmerella bacillaris (12.9 %). Technological characterization highlighted several inter- and intra-species differences. The best oenological aptitude was highlighted for species Starm. bacillaris, Metschnikowia spp., Pichia kluyveri and Zygosaccharomyces bailli. The best fermentation performances in laboratory-scale fermentations were found for Starm. bacillaris and P. kluyveri, due to their ability to reduce ethanol (-0.34 % v/v) and enhance glycerol production (+0.46 g/L). This behavior was further confirmed in winery. Results of this study contribute to the knowledge of yeast communities associated with a specific environment, like those of Valtellina wine region.
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Affiliation(s)
- Gabriele Serafino
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Paola Di Gianvito
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Simone Giacosa
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Domen Škrab
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Luca Cocolin
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Vasileios Englezos
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy.
| | - Kalliopi Rantsiou
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
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Taggart NT, Crabtree AM, Creagh JW, Bizarria R, Li S, de la Higuera I, Barnes JE, Shipley MA, Boyer JM, Stedman KM, Ytreberg FM, Rowley PA. Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae. PLoS Pathog 2023; 19:e1011418. [PMID: 37285383 PMCID: PMC10281585 DOI: 10.1371/journal.ppat.1011418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/20/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.
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Affiliation(s)
- Nathan T Taggart
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Angela M Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jack W Creagh
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Rodolfo Bizarria
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Shunji Li
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Ignacio de la Higuera
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - Jonathan E Barnes
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
| | - Mason A Shipley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Josephine M Boyer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Kenneth M Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - F Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Department of Physics, University of Idaho, Moscow, Idaho, United States of America
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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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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Zhao C, Li S, Ma Z, Wang W, Gao L, Han C, Yang A, Wu X. Anastomosis Groups and Mycovirome of Rhizoctonia Isolates Causing Sugar Beet Root and Crown Rot and Their Sensitivity to Flutolanil, Thifluzamide, and Pencycuron. J Fungi (Basel) 2023; 9:jof9050545. [PMID: 37233256 DOI: 10.3390/jof9050545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Anastomosis groups (AGs) or subgroups of 244 Rhizoctonia isolates recovered from sugar beet roots with symptoms of root and crown rot were characterized to be AG-A, AG-K, AG-2-2IIIB, AG-2-2IV, AG-3 PT, AG-4HGI, AG-4HGII, and AG-4HGIII, with AG-4HGI (108 isolates, 44.26%) and AG-2-2IIIB (107 isolates, 43.85%) being predominate. Four unclassified mycoviruses and one hundred and one putative mycoviruses belonging to six families, namely Mitoviridae (60.00%), Narnaviridae (18.10%), Partitiviridae (7.62%), Benyviridae (4.76%), Hypoviridae (3.81%), and Botourmiaviridae (1.90%), were found to be present in these 244 Rhizoctonia isolates, most of which (88.57%) contained positive single-stranded RNA genome. The 244 Rhizoctonia isolates were all sensitive to flutolanil and thifluzamide, with average median effective concentration (EC50) value of 0.3199 ± 0.0149 μg·mL-1 and 0.1081 ± 0.0044 μg·mL-1, respectively. Among the 244 isolates, except for 20 Rhizoctonia isolates (seven isolates of AG-A and AG-K, one isolate of AG-4HGI, and 12 isolates of AG-4HGII), 117 isolates of AG-2-2IIIB, AG-2-2IV, AG-3 PT, and AG-4HGIII, 107 isolates of AG-4HGI, and six isolates of AG-4HGII were sensitive to pencycuron, with average EC50 value of 0.0339 ± 0.0012 μg·mL-1. Correlation index (ρ) of cross-resistance level between flutolanil and thifluzamide, flutolanil and pencycuron, and thifluzamide and pencycuron was 0.398, 0.315, and 0.125, respectively. This is the first detailed study on AG identification, mycovirome analysis, and sensitivity to flutolanil, thifluzamide, and pencycuron of Rhizoctonia isolates associated with sugar beet root and crown rot.
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Affiliation(s)
- Can Zhao
- College of Plant Protection, China Agricultural University, Beijing 100193, China
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Siwei Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhihao Ma
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wenjun Wang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Lihong Gao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Anpei Yang
- Institute of Plant Protection, Xinjiang Academy of Agricultural Science, Urumqi 830091, China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
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Servienė E, Serva S. Recent Advances in the Yeast Killer Systems Research. Microorganisms 2023; 11:1191. [PMID: 37317165 DOI: 10.3390/microorganisms11051191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 06/16/2023] Open
Abstract
Biocidic phenotype is common in yeast strains isolated from a variety of natural and industrial habitats [...].
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Affiliation(s)
- Elena Servienė
- Laboratory of Genetics, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
| | - Saulius Serva
- Laboratory of Nucleic Acid Biochemistry, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, 10257 Vilnius, Lithuania
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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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De Miccolis Angelini RM, Raguseo C, Rotolo C, Gerin D, Faretra F, Pollastro S. The Mycovirome in a Worldwide Collection of the Brown Rot Fungus Monilinia fructicola. J Fungi (Basel) 2022; 8:jof8050481. [PMID: 35628739 PMCID: PMC9147972 DOI: 10.3390/jof8050481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
The fungus Monilinia fructicola is responsible for brown rot on stone and pome fruit and causes heavy yield losses both pre- and post-harvest. Several mycoviruses are known to infect fungal plant pathogens. In this study, a metagenomic approach was applied to obtain a comprehensive characterization of the mycovirome in a worldwide collection of 58 M. fructicola strains. Deep sequencing of double-stranded (ds)RNA extracts revealed a great abundance and variety of mycoviruses. A total of 32 phylogenetically distinct positive-sense (+) single-stranded (ss)RNA viruses were identified. They included twelve mitoviruses, one in the proposed family Splipalmiviridae, and twelve botourmiaviruses (phylum Lenarviricota), eleven of which were novel viral species; two hypoviruses, three in the proposed family Fusariviridae, and one barnavirus (phylum Pisuviricota); as well as one novel beny-like virus (phylum Kitrinoviricota), the first one identified in Ascomycetes. A partial sequence of a new putative ssDNA mycovirus related to viruses within the Parvoviridae family was detected in a M. fructicola isolate from Serbia. The availability of genomic sequences of mycoviruses will serve as a solid basis for further research aimed at deepening the knowledge on virus–host and virus–virus interactions and to explore their potential as biocontrol agents against brown rot disease.
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