Virion-associated nucleic acid-based metagenomics: A decade of advances in molecular characterization of plant viruses

Moubset Oumaima, François Sarah, Maclot François, Palanga Essowé, Julian Charlotte, Claude Lisa, Fernandez Emmanuel, Rott Philippe, Daugrois Jean-Heinrich, Antoine-Lorquin Aymeric, Bernardo Pauline, Blouin Arnaud G., Temple Coline, Kraberger Simona, Fontenele Rafaela S, Harkins Gordon William, Ma Yuxin, Marais Armelle, Candresse Thierry, Ben Chehida Sélim, Lefeuvre Pierre, Lett Jean-Michel, Varsani Arvind, Massart Sébastien, Ogliastro Mylène, Martin Darren Patrick, Filloux Denis, Roumagnac Philippe. 2022. Virion-associated nucleic acid-based metagenomics: A decade of advances in molecular characterization of plant viruses. Phytopathology, 112 (11) : 2253-2272.

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie

Résumé : 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.

Mots-clés Agrovoc : virus des végétaux, identification, génomique

Mots-clés libres : Ecology, Pathogen detection, Virology

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Regional Development Fund, European Commission

Agences de financement hors UE : Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Agence Nationale de la Recherche, Conseil Régional de La Réunion, Belgian Federal Public Service of Health, Food Chain Safety

Programme de financement européen : H2020

Projets sur financement : (FRA) Mesure et cartographie de la richesse des virus des plante à l'échelle de l'écosytème, (EU) Innovative Network for Next Generation Training and Sequencing of Virome

Auteurs et affiliations

• Moubset Oumaima, CIRAD-BIOS-UMR PHIM (FRA)
• François Sarah, University of Oxford (GBR)
• Maclot François, GxABT (BEL)
• Palanga Essowé, ITRA (TGO)
• Julian Charlotte, CIRAD-BIOS-UMR PHIM (FRA)
• Claude Lisa, Université de Montpellier (FRA)
• Fernandez Emmanuel, CIRAD-BIOS-UMR PHIM (FRA)
• Rott Philippe, CIRAD-BIOS-UMR PHIM (FRA) ORCID: 0000-0001-6085-6159
• Daugrois Jean-Heinrich, CIRAD-BIOS-UMR PHIM (FRA)
• Antoine-Lorquin Aymeric, Université de Montpellier (FRA)
• Bernardo Pauline, Enza Zaden (NLD)
• Blouin Arnaud G., GxABT (BEL)
• Temple Coline, ITRA (TGO)
• Kraberger Simona, Arizona State University (USA)
• Fontenele Rafaela S, Arizona State University (USA)
• Harkins Gordon William, University of the Western Cape (ZAF)
• Ma Yuxin, Université de Bordeaux (FRA)
• Marais Armelle, INRAE (FRA)
• Candresse Thierry, INRAE (FRA)
• Ben Chehida Sélim, CIRAD-BIOS-UMR PVBMT (REU)
• Lefeuvre Pierre, CIRAD-BIOS-UMR PVBMT (REU)
• Lett Jean-Michel, CIRAD-BIOS-UMR PVBMT (REU)
• Varsani Arvind, Arizona State University (USA)
• Massart Sébastien, GxABT (BEL)
• Ogliastro Mylène, University of Oxford (GBR)
• Martin Darren Patrick, UCT (ZAF)
• Filloux Denis, CIRAD-BIOS-UMR PHIM (FRA)
• Roumagnac Philippe, CIRAD-BIOS-UMR PHIM (FRA) ORCID: 0000-0001-5002-6039 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/603617/)

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