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Thesis started, 2016 - Defended in 2018, December 2018, 7^th
Fund:  MESR
Direction: Jean-Christophe Simon, Claire Lemaitre (IRISA), Christophe Mougel

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Abstract : 

Host-microbiota interactions are ubiquitous, and play a major role in the life of every organisms. The rise of metagenomic sequencing allows to characterize these associations with an unprecedented resolution, and to tackle the structure function and evolutionary history of these associations. This thesis aims at taking the full advantage of this technology by applying it to a well-known model of insect host-symbiont relationships : the pea aphid. The contributions are shared between insights on the pea aphid microbiome, structure end evolution, and the development of new tools for a fine-scale analysis of metagenomic diversity. Using resequencing data, we highlighted an unsuspected diversity for the pea aphid symbionts, that we linked to contrasted evolutionary histories. In a second time, we present an innovative approach for genome assembly in metagenomic complex, that takes advantage of existing genomes to facilitate the assembly. The method is very suitable for the discovery of metagenomic structural variations, as highlighted by the assembly of bacteriophage variants. Altogether, this work brings new insights on the pea aphid microbiome, and present new methods that may be applied to more complex systems.

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