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Massé D, Candresse T, Filloux D, Massart S, Cassam N, Hostachy B, Marais A, Fernandez E, Roumagnac P, Verdin E, Teycheney PY, Lett JM, Lefeuvre P. Characterization of Six Ampeloviruses Infecting Pineapple in Reunion Island Using a Combination of High-Throughput Sequencing Approaches. Viruses 2024; 16:1146. [PMID: 39066307 PMCID: PMC11281624 DOI: 10.3390/v16071146] [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: 06/19/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The cultivation of pineapple (Ananas comosus) is threatened worldwide by mealybug wilt disease of pineapple (MWP), whose etiology is not yet fully elucidated. In this study, we characterized pineapple mealybug wilt-associated ampeloviruses (PMWaVs, family Closteroviridae) from a diseased pineapple plant collected from Reunion Island, using a high-throughput sequencing approach combining Illumina short reads and Nanopore long reads. Reads co-assembly resulted in complete or near-complete genomes for six distinct ampeloviruses, including the first complete genome of pineapple mealybug wilt-associated virus 5 (PMWaV5) and that of a new species tentatively named pineapple mealybug wilt-associated virus 7 (PMWaV7). Short reads data provided high genome coverage and sequencing depths for all six viral genomes, contrary to long reads data. The 5' and 3' ends of the genome for most of the six ampeloviruses could be recovered from long reads, providing an alternative to RACE-PCRs. Phylogenetic analyses did not unveil any geographic structuring of the diversity of PMWaV1, PMWaV2 and PMWaV3 isolates, supporting the current hypothesis that PMWaVs were mainly spread by human activity and vegetative propagation.
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Affiliation(s)
- Delphine Massé
- ANSES—LSV RAPT, F-97410 St. Pierre, La Réunion, France; (N.C.); (B.H.)
- UMR PVBMT, Université de La Réunion, F-97410 St. Pierre, La Réunion, France
| | - Thierry Candresse
- INRAe, UMR 1332 Biologie du Fruit et Pathologie, Université Bordeaux, CS20032, F-33882 Villenave d’Ornon, France; (T.C.); (A.M.)
| | - Denis Filloux
- CIRAD, UMR PHIM, F-34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34090 Montpellier, France
| | - Sébastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium;
| | - Nathalie Cassam
- ANSES—LSV RAPT, F-97410 St. Pierre, La Réunion, France; (N.C.); (B.H.)
| | - Bruno Hostachy
- ANSES—LSV RAPT, F-97410 St. Pierre, La Réunion, France; (N.C.); (B.H.)
| | - Armelle Marais
- INRAe, UMR 1332 Biologie du Fruit et Pathologie, Université Bordeaux, CS20032, F-33882 Villenave d’Ornon, France; (T.C.); (A.M.)
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, F-34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34090 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, F-34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34090 Montpellier, France
| | - Eric Verdin
- INRAe, UR407 Unité de Pathologie Végétale, CS 60094, F-84140 Montfavet, France;
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, F-97410 St. Pierre, La Réunion, France; (P.-Y.T.); (J.-M.L.); (P.L.)
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, F-97410 St. Pierre, La Réunion, France; (P.-Y.T.); (J.-M.L.); (P.L.)
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, F-97410 St. Pierre, La Réunion, France; (P.-Y.T.); (J.-M.L.); (P.L.)
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Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, Massart S. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Front Microbiol 2023; 14:1181562. [PMID: 37323908 PMCID: PMC10265641 DOI: 10.3389/fmicb.2023.1181562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
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Affiliation(s)
| | - Maryam Khalili
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
- EGFV, Univ. Bordeaux, INRAE, ISVV, Villenave d’Ornon, France
| | | | - Mark Paul S. Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- College of Agriculture and Agri-Industries, Caraga State University, Butuan, Philippines
| | - Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- DNAVision (Belgium), Charleroi, Belgium
| | - Ferran Salavert
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Coline Temple
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Spain
| | - Neil Boonham
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), Wageningen, Netherlands
| | | | - Adrian Fox
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
- Fera Science Ltd, York Biotech Campus, York, United Kingdom
| | | | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ilhem Selmi
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachid Tahzima
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Plant Sciences Unit, Institute for Agricultural, Fisheries and Food Research (ILVO), Merelbeke, Belgium
| | - Charlotte Trontin
- European and Mediterranean Plant Protection Organization, Paris, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Bioversity International, Montpellier, France
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Ishwara Bhat A, Selvarajan R, Balasubramanian V. Emerging and Re-Emerging Diseases Caused by Badnaviruses. Pathogens 2023; 12:pathogens12020245. [PMID: 36839517 PMCID: PMC9963457 DOI: 10.3390/pathogens12020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops.
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Affiliation(s)
- Alangar Ishwara Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Ramasamy Selvarajan
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
| | - Velusamy Balasubramanian
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
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Rumbou A, Vainio EJ, Büttner C. Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems. Microorganisms 2021; 9:microorganisms9081730. [PMID: 34442809 PMCID: PMC8399312 DOI: 10.3390/microorganisms9081730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.
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Affiliation(s)
- Artemis Rumbou
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
- Correspondence:
| | - Eeva J. Vainio
- Natural Resources Institute Finland, Forest Health and Biodiversity, Latokartanonkaari 9, 00790 Helsinki, Finland;
| | - Carmen Büttner
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
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