Virion-associated nucleic acid-based metagenomics: a decade of advances in molecular characterization of plant viruses
Oumaima Moubset
(1, 2)
,
Sarah François
(3)
,
François Maclot
(4)
,
Essowè Palanga
(5)
,
Charlotte Julian
(1, 2)
,
Lisa Claude
(1)
,
Emmanuel Fernandez
(1, 2)
,
Philippe C Rott
(2, 1)
,
Jean Heinrich Daugrois
(1, 2)
,
Aymeric Antoine-Lorquin
(6)
,
Pauline Bernardo
(7)
,
Arnaud Blouin
(4, 8)
,
Coline Temple
(4)
,
Simona Kraberger
(9)
,
Rafaela Fontenele
(9)
,
Gordon Harkins
(10)
,
Yuxin Ma
(11)
,
Armelle Marais
(11)
,
Thierry Candresse
(11)
,
Sélim Ben Chéhida
(12, 2)
,
Pierre Lefeuvre
(12, 2)
,
Jean-Michel Lett
(12, 2)
,
Arvind Varsani
(9, 13)
,
Sébastien Massart
(4)
,
Mylene Ogliastro
(6)
,
Darren Martin
(13)
,
Denis Filloux
(1, 2)
,
Philippe Roumagnac
(1, 2)
1
UMR PHIM -
Plant Health Institute of Montpellier
2 Cirad-BIOS - Département Systèmes Biologiques
3 University of Oxford
4 Gembloux Agro-Bio Tech [Gembloux]
5 ITRA - Institut Togolais de Recherche Agronomique
6 DGIMI - Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier]
7 Enza Zaden
8 Agroscope
9 ASU - Arizona State University [Tempe]
10 UWC - University of the Western Cape
11 BFP - Biologie du fruit et pathologie
12 UMR PVBMT - Peuplements végétaux et bioagresseurs en milieu tropical
13 University of Cape Town
2 Cirad-BIOS - Département Systèmes Biologiques
3 University of Oxford
4 Gembloux Agro-Bio Tech [Gembloux]
5 ITRA - Institut Togolais de Recherche Agronomique
6 DGIMI - Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier]
7 Enza Zaden
8 Agroscope
9 ASU - Arizona State University [Tempe]
10 UWC - University of the Western Cape
11 BFP - Biologie du fruit et pathologie
12 UMR PVBMT - Peuplements végétaux et bioagresseurs en milieu tropical
13 University of Cape Town
Sarah François
- Fonction : Auteur
- PersonId : 1321413
- IdHAL : sarah-francois
- ORCID : 0000-0002-1138-8800
Lisa Claude
- Fonction : Auteur
- PersonId : 800876
- ORCID : 0000-0002-0418-5888
Philippe C Rott
- Fonction : Auteur
- PersonId : 937676
Jean Heinrich Daugrois
- Fonction : Auteur
- PersonId : 1178971
- ORCID : 0000-0002-7282-5859
Armelle Marais
- Fonction : Auteur
- PersonId : 740106
- IdHAL : armelle-marais
- ORCID : 0000-0003-2482-1543
- IdRef : 25311957X
Thierry Candresse
- Fonction : Auteur
- PersonId : 741063
- IdHAL : thierry-candresse
- ORCID : 0000-0001-9757-1835
- IdRef : 058616438
Pierre Lefeuvre
- Fonction : Auteur
- PersonId : 1339089
- ORCID : 0000-0003-2645-8098
Jean-Michel Lett
- Fonction : Auteur
- PersonId : 1153049
- ORCID : 0000-0003-2013-0016
Mylene Ogliastro
- Fonction : Auteur
- PersonId : 740527
- IdHAL : mylene-ogliastro
- ORCID : 0000-0003-4841-7043
- IdRef : 167635050
Philippe Roumagnac
- Fonction : Auteur
- PersonId : 802733
- ORCID : 0000-0001-5002-6039
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 (2010-2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsid-less 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.
Domaines
Biodiversité et Ecologie Sciences du Vivant [q-bio] Zoologie des invertébrés Organisation et fonctions cellulaires [q-bio.SC] VirologieFormat du dépôt | Fichier |
---|---|
Type de dépôt | Article dans une revue |
Titre |
en
Virion-associated nucleic acid-based metagenomics: a decade of advances in molecular characterization of plant viruses
|
Résumé |
en
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 (2010-2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsid-less 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.
|
Auteur(s) |
Oumaima Moubset
1, 2
, Sarah François
3
, François Maclot
4
, Essowè Palanga
5
, Charlotte Julian
1, 2
, Lisa Claude
1
, Emmanuel Fernandez
1, 2
, Philippe C Rott
2, 1
, Jean Heinrich Daugrois
1, 2
, Aymeric Antoine-Lorquin
6
, Pauline Bernardo
7
, Arnaud Blouin
4, 8
, Coline Temple
4
, Simona Kraberger
9
, Rafaela Fontenele
9
, Gordon Harkins
10
, Yuxin Ma
11
, Armelle Marais
11
, Thierry Candresse
11
, Sélim Ben Chéhida
12, 2
, Pierre Lefeuvre
12, 2
, Jean-Michel Lett
12, 2
, Arvind Varsani
9, 13
, Sébastien Massart
4
, Mylene Ogliastro
6
, Darren Martin
13
, Denis Filloux
1, 2
, Philippe Roumagnac
1, 2
1
UMR PHIM -
Plant Health Institute of Montpellier
( 1100829 )
- CIRAD Campus International de Baillarguet TA A-54/K
34398 Montpellier
- France
2
Cirad-BIOS -
Département Systèmes Biologiques
( 168219 )
- Avenue Agropolis TA A-DIR / 04 34398 Montpellier Cedex 5 France
- France
3
University of Oxford
( 302612 )
- Wellington Square, Oxford OX1 2JD
- Royaume-Uni
4
Gembloux Agro-Bio Tech [Gembloux]
( 491190 )
- Passage des Déportés, 2
B-5030 Gembloux
- Belgique
5
ITRA -
Institut Togolais de Recherche Agronomique
( 313736 )
- Lomé
- Togo
6
DGIMI -
Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier]
( 1100775 )
- Place Eugène Bataillon 34095 Montpellier cedex 5
- France
7
Enza Zaden
( 1045789 )
- Enkhuize
- Pays-Bas
8
Agroscope
( 1051931 )
- Berne
- Suisse
9
ASU -
Arizona State University [Tempe]
( 251827 )
- 325 E Apache Blvd, Tempe, AZ 85281, États-Unis
- États-Unis
10
UWC -
University of the Western Cape
( 491523 )
- Robert Sobukwe Road, Bellville, 7535, Republic of South Africa
- Afrique du Sud
11
BFP -
Biologie du fruit et pathologie
( 1002364 )
- Centre INRAE Bordeaux-Aquitaine 71 avenue Bourlaux BP81 F-33883 Villenave d'Ornon
- France
12
UMR PVBMT -
Peuplements végétaux et bioagresseurs en milieu tropical
( 1001933 )
- Faculté des Sciences et techniques - Université de La Réunion 15 avenue René Cassin CS92003 97744 Saint-Denis Cédex 9 pour le Cirad Station de Ligne-Paradis - 7 chemin de l'IRAT - 97410 Saint-Pierre
- La Réunion
13
University of Cape Town
( 303907 )
- Private Bag X3, Rondebosch 7701, South Africa
- Afrique du Sud
|
Licence |
Paternité - Pas d'utilisation commerciale - Pas de modification
|
Langue du document |
Anglais
|
Nom de la revue |
|
Vulgarisation |
Non
|
Comité de lecture |
Oui
|
Date de publication |
2022-12-28
|
Audience |
Internationale
|
Volume |
112
|
Numéro |
11
|
Page/Identifiant |
2253-2272
|
Version du document |
version éditeur
|
Public visé |
Scientifique
|
Sous-type de document pour les Articles |
Research article
|
Domaine(s) |
|
Thésaurus Inrae |
|
Projet(s) ANR |
|
Projet(s) Européen(s) |
|
Financement |
|
Mots-clés |
en
Ecology, Pathogen Detection, Virology
|
DOI | 10.1094/PHYTO-03-22-0096-RVW |
Pubmed Id | 35722889 |
UT key WOS | 000952321600002 |
Origine :
Fichiers éditeurs autorisés sur une archive ouverte
Licence : Paternité - Pas d'utilisation commerciale - Pas de modification - CC BY 4.0
Licence : Paternité - Pas d'utilisation commerciale - Pas de modification - CC BY 4.0
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