Exploring within-host diversity of plant viruses in rice agrosystems using two high-throughput sequencing strategies

Poulicard Nils, Dereeper Alexis, Pinel-Galzi Agnès, Fernandez Emmanuel, Julian Charlotte, Hubert Judith, Filloux Denis, Fargette Denis, Roumagnac Philippe, Hebrard Eugénie. 2019. Exploring within-host diversity of plant viruses in rice agrosystems using two high-throughput sequencing strategies. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 34. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.

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Abstract : The recent advances in high-throughput sequencing (HTS) has proven efficient for characterizing within-host diversity of several viruses, which has shed light on the influence of this diversity on the global fitness and virulence of viruses. We here aimed at evaluating the impact of rice management on the within-host diversity of Rice yellow mottle virus (RYMV) in order to optimize the cultural practices and to limit the burden of Rice yellow mottle disease in Africa. We worked on rice plants collected from traditional and intensive rice fields in East Africa, which is the center of origin of Rice yellow mottle virus. Interestingly, several strains with contrasted pathogenic and epidemiological parameters co-exist in this region and recombination events between strains were identified recently. We selected twelve RYMV symptomatic samples from fields managed under different types of practices that were analyzed using two HTS strategies: a metagenomics-based approach and a RYMV specific sequencing approach. Combining both strategies, we tested if the RYMV was associated with other viral species in rice, and if some cases of co-infections between RYMV strains occurred. Both approaches indicate a significant within-host RYMV diversity, which allows us to perceive the diversification processes of RYMV strains at the field scale. The detection of recombinants and the comparison of the within-host genetic diversity depending on the cultivation practices are underway.

Auteurs et affiliations

  • Poulicard Nils, IRD (FRA)
  • Dereeper Alexis, IRD (FRA)
  • Pinel-Galzi Agnès, IRD (FRA)
  • Fernandez Emmanuel, CIRAD-BIOS-UMR BGPI (FRA)
  • Julian Charlotte, CIRAD-BIOS-UMR BGPI (FRA)
  • Hubert Judith, SUA (TZA)
  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Fargette Denis, IRD (MEX)
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-5002-6039
  • Hebrard Eugénie, IRD (FRA)

Source : Cirad-Agritrop (

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