The plant epigenome is at the base of intraspecific variation and environmental adaptation. DNA methylation and histone modification patterns lead to chromatin alteration and transposable element (TE) silencing. To assess TE insertion polymorphisms, I am using PacBio HiFi reads for generating chromosome-level genome assemblies of different Arabidopsis thaliana accessions. I am integrating these genomes with epigenetic variation data from wildtypes and mutants defective for epigenetic pathways. This intersection will shed light onto chromatin and TE dynamics.