DOI: 10.5061/dryad.0p2ngf24b
title: CENH3 information from: Einkorn genomics sheds light on history of the oldest domesticated wheat

description: 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.
description: Chromatin immunoprecipitation (ChIP) and sequencing
 (ChIP-seq): Chromatin immunoprecipitation (ChIP) was performed according
 to the method given by Nagaki <em>et al</em>. 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: Raw ChIP sequencing reads were quality filtered and adapter
 sequences were removed with trimmomatic using LEADING:3 TRAILIN G:3
 SLIDINGWINDOW:4:20 MINLEN:50. Trimmed reads were then mapped to the
 respective genomes using bowtie2 with the following parameters:
 --score-min L,-0.6,-0.25. The sam output file was converted to bam format,
 the reads were sorted by position, and duplicates were removed using
 SAMtools (v1.8). Multi-mappers were allowed to include reads that come
 from highly repetitive regions. The resulting bam file was filtered using
 samtools view with the -h flag and the command grep -e $'^@' -e
 $'\t151M\t=' -e $'\t150M\t=' to only keep reads that
 have no mismatch over the full read length, which can be either 150bp or
 151bp long. The filtered bam files were indexed using samtools index with
 the -c flag and read depth per base was calculated using samtools depth
 with the -a flag to also report positions with no mapped reads. The
 resulting depth per base was then averaged in non-overlapping 100kb
 windows. The resulting CENH3 Chip-seq read coverage
 plots were the used to define boundaries of functional centromeres.
 Boundaries were determined by eye, as the regions when CENH3 coverage
 sharply increased and decreased, respectively. Boundaries were defined
 with a resolution of 100 kb. To assess the contiguous assembly of the
  centromeres, we obtained the breakpoints (start and end) of each contig
 in the pseudomolecule assemblies using MUMmer (v4.0.0.2). We then mapped
 the contig breakpoints with the CENH3 read density to see whether the
 centromeres are contained on a single contig.
description: The link contain the BED files and the BAM (mapped) files of
 CENH3 reads against the respective genome assembly.