Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18]

Teycheney Pierre-Yves, Bandou Eric, Gomez Rose-Marie, Lange David, Pavis Claudie, Umber Marie, Acina Manbole Isabelle Nina, Bonheur Lydiane, Daugrois Jean-Heinrich, Fernandez Emmanuel, Filloux Denis, Julian Charlotte, Roumagnac Philippe, Grisoni Michel, Pierret Alycia, Rubington Margot, Candresse Thierry, Contreras Sandy, Faure Chantal, Marais Armelle, Theil Sébastien, Da Câmara Machado Artur, Mendonça Duarte, Pinheiro de Carvalho Miguel A.A., Silva Emanuel. 2015. Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18]. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 30. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.

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Abstract : A comparative assay of 8 viral metagenomic protocols based on next generation sequencing (NGS) was performed on 6 tropical and subtropical crops (banana, garlic, sugarcane, sweet potato, vanilla and yam) originating from the Azores, Guadeloupe, Madeira and Réunion. Roche 454-based sequencing of purified dsRNA and virion-associated nucleic acids (VANA) proved the best strategies for recovering plant virus sequences following a first screening performed on a set of 96 plant samples. These two metagenomics approaches were further used on a total of 740 plant samples of the 6 targeted crops. Following demultiplexing, reads were either mapped against viral references or assembled into contigs and annotated using Blast analyses, leading to the identification and molecular characterization of 5 new viral species in garlic, 10 in yams, 7 in sugarcane, and 3 in vanilla. Sequences hinting at the possible presence of additional novel agents were also identified. In addition, a systematic search was performed on publicly available EST resources for the 6 targeted crops in order to identify yet uncharacterized viral agents. For all newly identified viruses, corresponding EST sequences were downloaded, assembled in contigs and taxonomic relationships were established. Sequences assembled from NGS reads and EST datamining were used to design specific primers for the detection of the novel viral species, allowing studies of their prevalence and diversity in germplasm collections conserved in European outermost regions and providing insights into transmission modes of some of these novel viruses. The potential of metagenomics for plant virus discovery and diagnostics will be discussed, together with the risk of complicating the exchange of plant materiel following the discovery of new virus species in conserved plant germplasm. (Résumé d'auteur)

Classification Agris : H20 - Plant diseases

Auteurs et affiliations

  • Teycheney Pierre-Yves, CIRAD-BIOS-UMR AGAP (GLP) ORCID: 0000-0002-9754-0745
  • Bandou Eric, INRA (GLP)
  • Gomez Rose-Marie, INRA (GLP)
  • Lange David, INRA (GLP)
  • Pavis Claudie, INRA (GLP)
  • Umber Marie, INRA (GLP)
  • Acina Manbole Isabelle Nina, CIRAD-BIOS-UMR AGAP (GLP)
  • Bonheur Lydiane
  • Daugrois Jean-Heinrich, CIRAD-BIOS-UMR BGPI (FRA)
  • Fernandez Emmanuel, CIRAD-BIOS-UMR BGPI (FRA)
  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Julian Charlotte, CIRAD-BIOS-UMR BGPI (FRA)
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (ZAF) ORCID: 0000-0001-5002-6039
  • Grisoni Michel, CIRAD-BIOS-UMR PVBMT (REU)
  • Pierret Alycia
  • Rubington Margot
  • Candresse Thierry, INRA (FRA)
  • Contreras Sandy, INRA (FRA)
  • Faure Chantal, INRA (FRA)
  • Marais Armelle, INRA (FRA)
  • Theil Sébastien, INRA (FRA)
  • Da Câmara Machado Artur, University of the Azores (PRT)
  • Mendonça Duarte, University of the Azores (PRT)
  • Pinheiro de Carvalho Miguel A.A., University of Madeira (PRT)
  • Silva Emanuel, University of Madeira (PRT)

Source : Cirad - Agritrop (

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