A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes

Abstract

AbstractEinkorn wheat (Triticum monococcum) is one of the oldest cereal crops to be domesticated by human beings, playing essential role in early agriculture development. Today, it is considered an important genomic resource for modern wheat improvement, especially for resistance against pests and diseases. However, the exploration and utilization of useful genes fromT. monococcumis limited due to the lack of a reference genome and annotation for this species. Here, we report a near-complete genome assembly forT. monococcumwith a total length of 5.11 Gb with a contig N50 of 131.2Mb and scaffold N50 of 728.66Mb, representing a genome assembly of highest quality for any wheat genome reported. Phylogenomic analysis confirmedT. monococcumis closely-related toT. urartu, the progenitor of wheat A subgenomes. A 4AL/5AL terminal translocation is present in the diploid speciesT. urartuandT. monococcum, taking place before wheat polyploidization.T. monococcumhas significantly expanded and unique gene families involved in DNA damage repair and heat stress tolerance, reflecting its adaptive evolution to cope with historical harsh climate in its natural habitat, South East Turkey. The genome sequence confirmed the introgression ofT. monococcumrust resistance genes at 5AmL into modern bread wheat varieties. This near-complete reference genome ofT. monococcumwill be an essential resource for wheat functional and evolutionary genomic studies and expedite the cloning of useful genes inT. monococcumfor future wheat improvement.