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Moubset O, Filloux D, Fontes H, Julian C, Fernandez E, Galzi S, Blondin L, Chehida SB, Lett JM, Mesléard F, Kraberger S, Custer JM, Salywon A, Makings E, Marais A, Chiroleu F, Lefeuvre P, Martin DP, Candresse T, Varsani A, Ravigné V, Roumagnac P. Virome release of an invasive exotic plant species in southern France. Virus Evol 2024; 10:veae025. [PMID: 38566975 PMCID: PMC10986800 DOI: 10.1093/ve/veae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.
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Affiliation(s)
- Oumaima Moubset
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Hugo Fontes
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Charlotte Julian
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Serge Galzi
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Laurence Blondin
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | | | | | - François Mesléard
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Salywon
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ 85008, USA
| | - Elizabeth Makings
- Vascular Plant Herbarium, School of Life Sciences, Arizona State University, 734 West Alameda Drive, Tempe Tempe, AZ 85282, USA
| | - Armelle Marais
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | | | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Cape Town 7925, South Africa
| | - Thierry Candresse
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7700, South Africa
| | - Virginie Ravigné
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
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Schönegger D, Moubset O, Margaria P, Menzel W, Winter S, Roumagnac P, Marais A, Candresse T. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. J Virol 2023; 97:e0130023. [PMID: 37888981 PMCID: PMC10688312 DOI: 10.1128/jvi.01300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
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Affiliation(s)
| | - Oumaima Moubset
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Wulf Menzel
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Stephan Winter
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
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3
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiol Mol Biol Rev 2022; 86:e0000421. [PMID: 35311574 PMCID: PMC9199400 DOI: 10.1128/mmbr.00004-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
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Affiliation(s)
- Juan Sebastián Andrade-Martínez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Carolina Camelo Valera
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luis Alberto Chica Cárdenas
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Forero-Junco
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Gamaliel López-Leal
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J. Leonardo Moreno-Gallego
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Guillermo Rangel-Pineros
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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5
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François S, Antoine-Lorquin A, Kulikowski M, Frayssinet M, Filloux D, Fernandez E, Roumagnac P, Froissart R, Ogliastro M. Characterisation of the Viral Community Associated with the Alfalfa Weevil ( Hypera postica) and Its Host Plant, Alfalfa ( Medicago sativa). Viruses 2021; 13:791. [PMID: 33925168 PMCID: PMC8145008 DOI: 10.3390/v13050791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 12/22/2022] Open
Abstract
Advances in viral metagenomics have paved the way of virus discovery by making the exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach opens new possibilities to explore how viruses circulate between insects and plants, which may help to optimise their management. It could also lead to identifying novel entomopathogenic viral resources potentially suitable for biocontrol strategies. We sampled the larvae of a natural population of alfalfa weevils (Hypera postica), a major herbivorous pest feeding on legumes, and its host plant alfalfa (Medicago sativa). Insect and plant samples were collected from a crop field and an adjacent meadow. We characterised the diversity and abundance of viruses associated with weevils and alfalfa, and described nine putative new virus species, including four associated with alfalfa and five with weevils. In addition, we found that trophic accumulation may result in a higher diversity of plant viruses in phytophagous pests compared to host plants.
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Affiliation(s)
- Sarah François
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Park Road, Oxford OX1 3SY, UK
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Aymeric Antoine-Lorquin
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Maximilien Kulikowski
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Marie Frayssinet
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Rémy Froissart
- MIVEGEC Infectious and Vector Diseases: Ecology, Genetics, Evolution and Control, University of Montpellier, CNRS, IRD, 34394 Montpellier, France;
| | - Mylène Ogliastro
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
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6
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Obbard DJ, Shi M, Roberts KE, Longdon B, Dennis AB. A new lineage of segmented RNA viruses infecting animals. Virus Evol 2020; 6:vez061. [PMID: 31976084 PMCID: PMC6966834 DOI: 10.1093/ve/vez061] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Mang Shi
- Charles Perkins Center, The University of Sydney, NSW 2006, Australia
| | - Katherine E Roberts
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Ben Longdon
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Alice B Dennis
- Department of Evolutionary Biology & Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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7
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Scussel S, Candresse T, Marais A, Claverie S, Hoareau M, Azali HA, Verdin E, Tepfer M, Filloux D, Fernandez E, Roumagnac P, Robène I, Lefeuvre P, Jourda C, Roux-Cuvelier M, Lett JM. High-throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago. Arch Virol 2019; 164:2193-2196. [PMID: 31123961 DOI: 10.1007/s00705-019-04228-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/05/2019] [Indexed: 11/26/2022]
Abstract
Using high-throughput sequencing of small interfering RNAs (siRNAs), virion-associated nucleic acid (VANA), and double stranded RNAs (dsRNAs), we have determined the complete genome sequences of Comorian isolates of two ipomoviruses, cassava brown streak virus (CBSV) and a divergent isolate of Ugandan cassava brown streak virus (UCBSV-KM) representing a new strain of this virus. While the large ORF of CBSV shares the highest nucleotide sequence identity (95.9%) with a Tanzanian isolate of CBSV, the large UCBSV-KM ORF shares the highest nucleotide sequence identity (77.5%) with a Malawian isolate of UCBSV. This low value is near the species demarcation threshold for the family Potyviridae (<76%). Phylogenetic analysis confirms that UCBSV-KM represents a new lineage that is genetically distinct from the currently described UCBSV strains.
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Affiliation(s)
- Sarah Scussel
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sohini Claverie
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
- Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | | | - Eric Verdin
- INRA, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
| | - Mark Tepfer
- INRA, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences (SPS), Université Paris-Saclay, 78026, Versailles, France
| | - Denis Filloux
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Emmanuel Fernandez
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Isabelle Robène
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Cyril Jourda
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Michel Roux-Cuvelier
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France.
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8
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Susi H, Filloux D, Frilander MJ, Roumagnac P, Laine AL. Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. PeerJ 2019; 7:e6140. [PMID: 30648011 PMCID: PMC6330959 DOI: 10.7717/peerj.6140] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.
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Affiliation(s)
- Hanna Susi
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
| | - Denis Filloux
- CIRAD, BGPI, Montpellier, France.,BGPI, INRA, CIRAD, SupAgro, University Montpellier, Montpellier, France
| | - Mikko J Frilander
- Institute of Biotechnology, Genome Biology Program, University of Helsinki, Finland
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRA, CIRAD, SupAgro, University Montpellier, Montpellier, France
| | - Anna-Liisa Laine
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
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9
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Obbard DJ. Expansion of the metazoan virosphere: progress, pitfalls, and prospects. Curr Opin Virol 2018; 31:17-23. [PMID: 30237139 DOI: 10.1016/j.coviro.2018.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/15/2018] [Accepted: 08/17/2018] [Indexed: 12/22/2022]
Abstract
Metagenomic sequencing has led to a recent and rapid expansion of the animal virome. It has uncovered a multitude of new virus lineages from under-sampled host groups, including many that break up long branches in the virus tree, and many that display unexpected genome sizes and structures. Although there are challenges to inferring the existence of a virus from a `virus-like sequence', in the absence of an isolate the analysis of nucleic acid (including small RNAs) and sequence data can provide considerable confidence. As a consequence, this period of molecular natural history is helping to reshape our views of deep virus evolution.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
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