Evolutionary dynamics of wheat D epigenome

To investigate whole-genome epigenetic dynamics among wheat subgenomes and different ploidies, we generated the histone maps for 19 histone marks using chromatin immunoprecipitation (ChIP) sequencing, including methylations (H3K4me1/2/3, H3K27me1/2/3, H3K9me2/3, H3K36me2/3, and H4K20me1), acetylations (H3K9ac, H3K18ac, H3K27ac, H3K56ac, H4K5ac), ubiquitination (H2Bub), histone H3 and centromere-specific histone H3 variant (CENH3) in young leaf tissues of Aikang58 (AK58), a modern wheat variety in china, and Aegilops tauschii AL8/78, the most likely wheat D-genome donor. We also established the genome-wide chromatin accessibility maps in leaves of AK58 and AL8/78 with differential micrococcal nuclease (MNase) sensitivity footprints (DNS). MNase difference was computed with the depth of coverage under light-digestion subtracted by that under heavy-digestion. We further defined the MNase hypersensitive regions (MNase HSs) to decipher open chromatin or accessible chromatin regions. In addition, we obtained the accessibilities in roots to explore the spatial dynamics for tissues.