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.

This link contains the following:

• Genome assemblies of two einkorn accessions: Triticum monococcum subsp. monococcum (accession: TA10622) and Triticum monococcum subsp. aegilpoides (accession: TA299). The two assemblies are chromosome-scale assemblies constructed using PacBio HiFi reads, bionano genomics optical map, and Omni-C proximity ligation.
• The annotation for both genomes.
• VCF file of 218 monococcum accessions called against TA299 reference assembly.
• The Nextera indices for the RILs population
• The CpG frequency files: TA299-ccsmeth-CpG-freq.bed.gz and TA10622-ccsmeth-CpG-freq.bed.gz