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

Poulicard N., Dereeper A., Pinel-Galzi A., Fernandez E., Julian C., Hubert J., Filloux D., Fargette D., Roumagnac P., Hebrard E.. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. Montpellier : International Phytobiomes Alliance; INRA, p. 68-68. International phytobiomes conference. 2, 2018-12-04/2018-12-06, Montpellier (France).

The virome is an essential component of the phytobiome as viruses correspond to the most abundant and diverse biological entity in Nature and interact with all living organisms. 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 between strains were identified recently. We selected twelve RYMV sympto-matic 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.

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