The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata. This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant selfing originated.Our results indicate that the mating system may be important for determining TE copy number, and that selfing species are likely to have fewer TEs.Transposable elements (TEs) are major contributors to genome evolution. They can replicate in a genome and therefore create genetic variation on a much larger scale than individual nucleotide changes [1]. Almost all eukaryotic genomes contain TEs but their TE content varies widely among genomes. An exception are many unicellular eukaryotic genomes which lack TEs [2]. TEs mainly use two different intermediates for their replication. Retrotransposons (class I elements) use an RNA intermediate for replication, whereas DNA transposons (class II elements) use a DNA intermediate [1]. Retrotransposons can be further subdivided into long terminal repeat (LTR) and non-LTR elements, based on the presence or absence of LTR sequences in the element.The evolutionary factors that influence TE abundance have received considerable attention [3-6]. One such factor is life history, such as whether a plant is a perennial or an annual [7-9]. Especially in weedy annuals, for example, selection may favor small genomes to reduce development time. This may indirectly lead to the elimination of TEs, because such elements may be more dispensab