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 effect of shifting from outcrossing to selfing, which occurs commonly in plants, is not known. To study how mating systems impact the dynamics of TE accumulation, we used the outcrossing species Arabidopsis lyrata which also has some North American populations that have recently experienced a shift to selfing. Specifically, we have sequenced from both selfing and outcrossing populations 20 genomes using long reads Oxford Nanopore Technology as well as 19 additional ones using short read Illumina sequencing. Using the short reads sequencing data, we have characterized the impact of selfing on genetic diversity as well as on the efficacy of purifying selection at the Single Nucleotide Polymorphism (SNP) level. After assembling the long-read sequenced genomes de novo, we have then detected transposable element insertion polymorphisms (TIPs) across these populations. We will discuss results from these analyses and how they inform us on the contribution of TEs to genetic diversity in relation to mating systems.