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Bioinformatique pour l’exploration de la diversité inter-espèces et inter-populations : hétérogénéité & données multi-omiques

Yannick Cogne 1
1 LI2D - Laboratoire Innovations technologiques pour la Détection et le Diagnostic
SPI - Service de Pharmacologie et Immunoanalyse : DRF/JOLIOT
Abstract : The exploitation of omics data combining transcriptomic and proteomic enables the detailed study of the molecular mechanisms of non-model organisms exposed to an environmental stress. The assembly of data from the RNA-seq of non-model organism enables to produce the protein database for the interpretation of spectra generated in shotgun proteomics. In this context, the aim of the PhD work was to optimize the interpretation and analysis of proteomic data through the development of innovative concepts for the construction of protein databases and the exploration of biodiversity. The first step focused on the development of a pretreatment method for RNA-seq data based on proteomic attribution results. The second step was to work on reducing the size of the databases by optimizing the parameters of the automated coding region search. The optimized method enabled the analysis of 7 taxonomic groups of Gammarids representative of the diversity found in natura. The proteomic databases thus produced enabled the inter-population analysis of 40 individual Gammarus pulex proteomes from two sampling sites (polluted vs reference). Statistical analysis based on an "individual" approach has shown an heterogeneity of the biological response within a population of organisms induced by an environmental stress. Different subclusters of molecular mechanisms response have been identified. Finally, the study of the transversality of the biomarkers peptides identified with Gammarus fossarum revealed which are the common ones using both proteomic and transcriptomic data. For this purpose, a software for the exploration of peptide sequences has been developed suggesting potential substitute biomarkers when the defined peptides are not available for some species of gammarids. All these concepts aim to improve the interpretation of data by proteogenomics. This work opens the door to the multi-omic analysis of individuals collected in natura by considering inter-species and intra-population biodiversity.
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Yannick Cogne. Bioinformatique pour l’exploration de la diversité inter-espèces et inter-populations : hétérogénéité & données multi-omiques. Médecine humaine et pathologie. Université Montpellier, 2019. Français. ⟨NNT : 2019MONTT033⟩. ⟨tel-02464655⟩

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