CENH3 information from: Einkorn genomics sheds light on history of the oldest domesticated wheat

Einkorn (Triticum monococcum) is the first domesticated wheat species, being central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent ~10,000 years ago. Here, we generate and analyze 5.2-gigabase genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions following the dispersal of domesticated einkorn from the Fertile Crescent. We also discovered that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat., Chromatin immunoprecipitation (ChIP) and sequencing (ChIP-seq): Chromatin immunoprecipitation (ChIP) was performed according to the method given by Nagaki et al. standardized with wheat CENH3 antibody. Nuclei were isolated from 2-week-old seedlings and digested with micrococcal nuclease (Sigma, MO) to liberate nucleosomes. The digested mixture was incubated overnight with 3 mg of wheat CENH3 antibody at 4°C. The chromatin-antibody complexes were captured using Dynabeads Protein G (Invitrogen, CA). Elution of the chromatin was done using 100 ml of preheated elution buffer (1% sodium dodecyl sulfate and 0.1 M NaHCO3) for 30 min at 65°C. DNA from the ChIP was isolated using ChIP DNA Clean and Concentrator Kit (Zymo Research, CA). ChIP-seq libraries were then constructed using the TruSeq ChIP Library Preparation Kit (Illumina, CA) according to the manufacturer’s instructions, and libraries were sequenced using NovoSeq S4 with 150-bp paired-end sequencing run.
CENH3 ChIP-seq data analysis: R..., The link contain the BED files and the BAM (mapped) files of CENH3 reads against the respective genome assembly.