MACLOT, François; CANDRESSE, Thierry; FILLOUX, Denis; MALMSTROM, Carolyn; ROUMAGNAC, Philippe; VAN DER VLUGT, René; MASSART, Sébastien

doi:10.3389/fmicb.2020.578064

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MACLOT, François
Université de Liège - Gembloux

CANDRESSE, Thierry
Biologie du fruit et pathologie [BFP]

FILLOUX, Denis
Biologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
Département Systèmes Biologiques [Cirad-BIOS]

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Frontiers in Microbiology. 2020, vol. 11, p. 578064

Frontiers Media

Résumé en anglais

The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.< Réduire

Mots clés

pathologie végétale

santé des plantes

Virologie végétale

Virus phytopathogène

Mots clés en anglais

virus ecology and evolution

plant virome

high throughput sequencing

historical advances

opportunities and challenges