Illuminating an ecological blackbox: Using high throughput sequencing to characterize the plant virome across scales

Maclot François, Candresse Thierry, Filloux Denis, Malmstrom Carolyn M., Roumagnac Philippe, van der Vlugt René, Massart Sébastien. 2020. Illuminating an ecological blackbox: Using high throughput sequencing to characterize the plant virome across scales. Frontiers in Microbiology, 11:578064, 16 p.

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Abstract : 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.

Mots-clés Agrovoc : Virus des végétaux, Relation hôte pathogène, Interactions biologiques, Écologie

Mots-clés complémentaires : séquençage haut débit, virome, Métagénomique

Mots-clés libres : Virus ecology and evolution, Plant virome, High throughput sequencing, Historical advances, Opportunities and challenges

Classification Agris : H20 - Plant diseases
F30 - Plant genetics and breeding
F40 - Plant ecology

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

Auteurs et affiliations

  • Maclot François, CIRAD-BIOS-UMR BGPI (FRA) - auteur correspondant
  • Candresse Thierry, INRAE (FRA)
  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Malmstrom Carolyn M., MSU (USA)
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-5002-6039
  • van der Vlugt René, Wageningen University (NLD)
  • Massart Sébastien, Université de Liège (BEL) - auteur correspondant

Source : Cirad-Agritrop (

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