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Toward the characterization of a novel Bymovirus infecting rice in Burkina Faso by combining metagenomics and targeted sequencing
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International audience. Toward the characterization of a novel Bymovirus infecting rice in Burkina Faso by combining metagenomics and targeted sequencingM. Bangratz1, M. Barro2, D. Sérémé2, I. Wonni2, A. I. Kassankogno2, P. Roumagnac1, D. Filloux1, E. Fernandez1, J. Orjuela1, A. Comte1, C. Tollenaere1* N. Poulicard1*1PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France; 2INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso. * equal contribution (martine.bangratz@ird.fr)Only two viruses have been described to infect rice in Africa, the rice yellow mottle virus (RYMV) and the rice stripe necrosis virus (RSNV). Using viral metagenomics, we aimed at exploring the diversity of viruses infecting rice in southwestern Burkina Faso. To this purpose, we collected rice samples in three irrigated perimeters and three rainfed lowland sites within two consecutive years (2016 and 2017). Within each site, 5-10 rice fields were surveved and 16 plants were sampled following a grid-based regular approach. The 16 samples collected within each rice field were pooled to constitute a ‘field-scale’ sample. Eighty-four of these ‘field scale’ samples were used for Virion-Associated Nucleic Acid (VANA) metagenomics-based approach and sequenced by Illumina HiSeq. Results revealed a number of reads related to unexpected viruses, among which one belongs to the genus Bymovirus (family Potyviridae), which shared ca. 80% nucleotidic identity with the rice necrosis mosaic virus (RNMV). RNMV is a bipartite (+)ssRNA virus (1) transmitted by the soil protist Polymyxa graminis and causes stunting and yellow lesions (2). Only a partial genome was retrieved from the novel bymovirus-like virus, as Illumina reads sharing identity with RNMV were scattered around the viral genome. Thus, we further combined Sanger and long-read sequencing (ONT Nanopore) to characterize the full viral genome of this novel rice virus. Preliminary results showed that the assembled complete genome shares 73% nucleotide homology with the published RNMV sequence, so we are certainly in presence of a new virus species of the genus Bymovirus infecting rice in Burkina Faso. In addition, we demonstrated by specific RT-PCR detection assays that this virus is present whatever the rice cultivation mode and widely distributed among the different sites. In perspective, we plan to better assess and understand the epidemiology of this new Bymovirus “RNMV like”-species in African rice fields.References(1)Wagh,S.G. et al., (2016). J Gen Plant Pathol 82 : 38-42(2)Ghosh,S.K. et al., (1981). Plant Disease 65 : 602-603
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