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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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Temple C, Blouin AG, Boezen D, Botermans M, Durant L, De Jonghe K, de Koning P, Goedefroit T, Minet L, Steyer S, Verdin E, Zwart M, Massart S. Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems. PHYTOPATHOLOGY 2024; 114:1680-1688. [PMID: 38648112 DOI: 10.1094/phyto-06-23-0194-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examined. This investigation led to the identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the time of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-third of such farms. However, outbreaks were sporadic and were associated at least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial.
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Affiliation(s)
- Coline Temple
- Plant Pathology Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Arnaud G Blouin
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Dieke Boezen
- Department of Microbial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700 AB, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive plants and Plant health, Netherlands Food and Product Safety Authority, Wageningen, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Laurena Durant
- Plant Pathology Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, 9820, Belgium
| | - Pier de Koning
- Netherlands Institute for Vectors, Invasive plants and Plant health, Netherlands Food and Product Safety Authority, Wageningen, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Thomas Goedefroit
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, 9820, Belgium
| | - Laurent Minet
- Hortiforum asbl/Centre Technique Horticole de Gembloux, Gembloux, Belgium
| | - Stephan Steyer
- Crops and Forest Health Unit, Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium
| | - Eric Verdin
- Unité de Pathologie Végétale, Institut National de Recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon, 84000, France
| | - Mark Zwart
- Department of Microbial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700 AB, The Netherlands
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Ghafari M, Sõmera M, Sarmiento C, Niehl A, Hébrard E, Tsoleridis T, Ball J, Moury B, Lemey P, Katzourakis A, Fargette D. Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathog 2024; 20:e1011911. [PMID: 38206964 PMCID: PMC10807823 DOI: 10.1371/journal.ppat.1011911] [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: 10/02/2023] [Revised: 01/24/2024] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
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Affiliation(s)
- Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annette Niehl
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Theocharis Tsoleridis
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Jonathan Ball
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Denis Fargette
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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