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Bread wheat (Triticum aestivum L.) is a major crop but advances in wheat genomics are facing the high complexity of its hexaploid genome, with a size of 17 Gb and composed of 85% of repetitive sequences derived from transposable elements (TEs). Because of this complexity, bread wheat is a model for studying the dynamics of TEs in genomes and their impact on plasticity. In order to get better insights into the understanding of these questions, we produced a unique resource, a reference sequence (pseudomolecule) of the largest wheat chromosomes, the 3B (880 Mb). The objectives of this thesis were to develop a new methodology for the automated TE modeling, to decipher the TE content and understand their dynamics and impact on the structure and evolution of the hexaploid wheat genome. We have developed a strategy implemented in a bioinformatics tool (CLARI-TE) dedicated to the automated TE modeling that is able to reconstruct nested TE insertions. In total, 252 000 TEs were predicted along the 774 Mb of the 3B pseudomolecule. Their heterogeneous distribution along the chromosome suggests a higher elimination rate in the distal recombinogenic regions compared to the proximal region. Discovery of structural variations associated with TEs has shown that the chromosomal extremities accumulated most of the inter- and intra-specific variability. We also revealed the extent of single gene duplications in wheat compared to the related grasses and we highlighted the significant association between CACTAs and duplicated genes, suggesting an important role of CACTAs in the recent adaptation of wheat.

Keywords: Transposable elements, bread wheat, annotation, genome evolution, gene duplication, CLARI-TE, CACTA.