Nanopore sequencing is a credible alternative to recover complete genomes of geminiviruses

Ben Chehida Sélim, Filloux Denis, Fernandez Emmanuel, Moubset Oumaima, Hoareau Murielle, Julian Charlotte, Blondin Laurence, Lett Jean-Michel, Roumagnac Philippe, Lefeuvre Pierre. 2021. Nanopore sequencing is a credible alternative to recover complete genomes of geminiviruses. Microorganisms, 9:903, 15 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Abstract : Next-generation sequencing (NGS), through the implementation of metagenomic protocols,has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocolsare still laborious and costly to implement, and the technique has not yet become routine for everydayvirus characterization. Within the context of CRESS DNA virus studies, we implemented twoalternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledgeof the viral genome) and the other that use specific primers to target a virus (with a priori). Agnosticand specific long read NGS-based assembled genomes of two capulavirus strains were compared tothose obtained using the gold standard technique of Sanger sequencing. Both protocols allowed thedetection and accurate full genome characterization of both strains. Globally, the assembled genomeswere very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in thehomopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGSapproach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has provento be a credible alternative in the context of CRESS DNA virus study and could offer a new range ofapplications not previously accessible.

Mots-clés Agrovoc : Géminivirus, Virus des végétaux, génomique, Génome

Mots-clés complémentaires : Séquencage, Capulavirus, Métagénomique, séquençage par nanopores, virus à ADN

Mots-clés libres : MinION, Nanopore sequencing, Rolling circle amplification, Viral metagenomics, CRESS DNA, Capulavirus, Homopolymer

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

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

Agence(s) de financement européenne(s) : European Commission, European Regional Development Fund

Auteurs et affiliations

  • Ben Chehida Sélim, CIRAD-BIOS-UMR PVBMT (REU)
  • Filloux Denis, CIRAD-BIOS-UMR PHIM (FRA)
  • Fernandez Emmanuel, CIRAD-BIOS-UMR PHIM (FRA)
  • Moubset Oumaima, CIRAD-BIOS-UMR PHIM (FRA)
  • Hoareau Murielle, CIRAD-BIOS-UMR PVBMT (REU)
  • Julian Charlotte, CIRAD-BIOS-UMR PHIM (FRA)
  • Blondin Laurence, CIRAD-BIOS-UMR PHIM (FRA)
  • Lett Jean-Michel, CIRAD-BIOS-UMR PVBMT (REU)
  • Roumagnac Philippe, CIRAD-BIOS-UMR PHIM (FRA) ORCID: 0000-0001-5002-6039
  • Lefeuvre Pierre, CIRAD-BIOS-UMR PVBMT (REU) - auteur correspondant

Source : Cirad-Agritrop (

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