Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant. [Display omitted] •Transcriptomes and methylomes from over 1,000 Arabidopsis accessions•>25% of genes show either gene-body or TE-like methylation states•Maximal sequence and methylation variation seen at immunity loci•Methylation strongly correlated with climate of origins and trans-acting variants Methylomes and transcriptomes from >1,000 Arabidopsis thaliana accessions provide insights on how the epigenome is shaped by natural genomic variation and by the environment.