Epigenomic and genome structural diversity in a worldwide collection of Arabidopsis thaliana

Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shaped the epigenome to allow rapid adaptation to environmental changes, with strong emphasis on disease resistance. Analysis of the cistromes and epicistromes in these accessions revealed a significant association between both methylation and nucleotide variation and the conservation of transcription factor binding sites. The Arabidopsis thaliana 1001 Epigenomes Project now provides a comprehensive resource to help further understand how epigenetic variation contributes to both molecular and phenotypes in natural populations of the most widely studied reference plant. Overall design: RNA-seq profiling of 728 Arabidopsis thaliana accessions Please note that the sample 'Cod-0 (9836)' is missing from the data columns in the normalized expression matrix ('ath1001_tx_norm_2016-04-21-UQ_gNorm_normCounts_k4.tsv') since the read count distribution from this sample was incompatible with the upper-quartile normalization method applied to all the samples, therefore excluded from the expression matrix.