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Nanopore-based detection and characterization of yam viruses

Filloux Denis, Fernandez Emmanuel, Loire Etienne, Claude Lisa, Galzi Serge, Candresse Thierry, Winter Stephan, Jeeva M.L., Makeshkumar T., Martin Darren Patrick, Roumagnac Philippe. 2018. Nanopore-based detection and characterization of yam viruses. Scientific Reports, 8:17879, 11 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q1, Sujet : MULTIDISCIPLINARY SCIENCES

Abstract : We here assessed the capability of the MinION sequencing approach to detect and characterize viruses infecting a water yam plant. This sequencing platform consistently revealed the presence of several plant virus species, including Dioscorea bacilliform virus, Yam mild mosaic virus and Yam chlorotic necrosis virus. A potentially novel ampelovirus was also detected by a complimentary Illumina sequencing approach. The full-length genome sequence of yam chlorotic necrosis virus was determined using Sanger sequencing, which enabled determination of the coverage and sequencing accuracy of the MinION technology. Whereas the total mean sequencing error rate of yam chlorotic necrosis virus-related MinION reads was 11.25%, we show that the consensus sequence obtained either by de novo assembly or after mapping the MinION reads on the virus genomic sequence was >99.8% identical with the Sanger-derived reference sequence. From the perspective of potential plant disease diagnostic applications of MinION sequencing, these degrees of sequencing accuracy demonstrate that the MinION approach can be used to both reliably detect and accurately sequence nearly full-length positive-sense single-strand polyadenylated RNA plant virus genomes.

Mots-clés Agrovoc : Patate douce, Virus, Séquence nucléotidique

Mots-clés complémentaires : Dioscorea bacilliform

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

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Fernandez Emmanuel, CIRAD-BIOS-UMR BGPI (FRA)
  • Loire Etienne, CIRAD-BIOS-UMR ASTRE (FRA)
  • Claude Lisa, CIRAD-BIOS-UMR BGPI (FRA)
  • Galzi Serge, CIRAD-BIOS-UMR BGPI (FRA)
  • Candresse Thierry, INRA (FRA)
  • Winter Stephan, Leibniz Institute DSMZ (DEU)
  • Jeeva M.L., ICAR (IND)
  • Makeshkumar T., ICAR (IND)
  • Martin Darren Patrick, Institute of Infectious Diseases and Molecular Medicine (ZAF)
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-5002-6039 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/590016/)

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