Genetic and epigenetic variation of transposable elements in Arabidopsis

•Natural Arabidopsis accessions exhibit genetic and epigenetic variation of TEs.•Variable enrichment of TE classes in euchromatin, pericentromeres and centromeres.•Different epigenetic pathways control TE expression, replication and recombination.•TEs play a major role in genome evolution and likely shape adaptive variation. Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation. Together, epigenetic modification and the forces of selection define the scope within which transposable elements can contribute to, and control, genome evolution.