Abstract
Genomic variation is induced by numerous factors simultaneously, which results in a set of genomic behaviours related to its structure, architecture, expression, evolution, etc, which could be referred to as genome dynamics. During my thesis project, we chose to focus on three major players impacting genome dynamics:- Chromatin structure: unevenly compacted along chromosomes;- Meiotic recombination landscape: reflecting the frequency variations of exchanging DNA fragments during cell division;- Repetitive DNA: mainly Transposable Elements (TEs) inducing genome assembly errors.Firstly, We propose an automated computational tool, based on the Marey maps method, allowing to identify heterochromatin boundaries along chromosomes and estimating local recombination rates. Our method, called BREC (heterochromatin Boundaries and RECombination rate estimates) is non-genome-specific, running even on non-model genomes as long as genetic and physical maps are available. BREC is a statistic-based data-driven tool. Therefore, a data pre-processing module (data quality control and cleaning) is provided. BREC results would allow conducting more broadly an analysis with a comparative genomics approach on their identified heterochromatin regions in terms of recombination landscape, TE density, etc.Secondly, in order to address the genome assembly process which is strongly impacted by the TE abundance, one type of repeats, we chose to focus on the scaffolding step with the aim of enhancing the assembly quality by exploiting the analysis of repeated regions and proposing a pipeline of improvement.Thirdly, with the aim of testing the veracity of the approaches and tools developed but also to return to the analysis of mosquito genomes, we present a case study combining the application results on the variations in recombination rate along these genomes, as well as and the organization of chromatin domains, with respect to the TE distribution along each chromosome. The preliminary findings suggest a correlation between the distribution of certain TE families and the chromatin domains.To conclude this thesis manuscript, we present an opening concerning genomes dynamics with respect to the different aspects addressed. Then, we present the conceptual, application, and technical limits identified by our experimental design. Finally, we suggest a few perspectives on the scope of our contributions beyond my PhD project.