Transposable elements (TEs) are now widely recognized as major contributors to genome evolution, yet the processes governing their accumulation remain elusive. Mating systems are expected to play a central role, but the net effect of the shift from outcrossing to selfing, which occurs commonly in plants, is not known. Here, we propose to determine the genomic landscape of recent TE insertions in the two outcrossing species Arabidopsis lyrata and A. halleri and to compare it to that of their selfing close relative A. thaliana as well as to that of North American A. lyrata populations that are currently experiencing a shift to selfing. This project is made possible by the advent of long reads sequencing technology, which enables the unambiguous characterization of TEs and other repeat sequences as well as of the complex regions in which they tend to cluster. Specifically, we will produce 100 high-quality genome sequence assemblies for A. lyrata and A. halleri. We will also compare the intensity of natural selection acting on new TE insertions between these three species. Finally, we will analyze the patterns and rate of accumulation of TEs in a key region of the genome, the S-locus, which controls self-incompatibility in outcrossing species. This region shows analogy to sex chromosomes because of a lack of recombination, very low sequence homology among self-incompatibility haplotypes, and high rate of TE accumulation. Our findings should provide major insights into how mating systems impact the accumulation of TEs. This project should also elucidate the role of TEs in driving the evolution of the mating system itself in the Brassicaceae through their rapid accumulation at the S-locus and their potential role in the generation of small RNAs controlling the dominance relationships among S-alleles. The methods and paradigms we will generate should have broad implications for the study of species with high level of heterozygosity and much larger genomes, including humans.