Common wheat (Triticum aestivum), one of the most widely cultivated and consumed food crops in the world, is a hexaploid containing A, B and D genomes. The A genome, as a basic genome of bread wheat and other polyploid wheats, plays a central role in wheat evolution, domestication and genetic improvement. T. urartu, a wild diploid wheat, is the progenitor of the wheat A genome. For studying the evolution and domestication of wheat, we have been working on the genome sequencing of T. urartu since 2009. First, we generated the draft genome of T. urartu using the whole-genome shotgun sequencing strategy on the Illumina HiSequation (2000) platform (Ling et al., 2013, Nature 496: 87-90). Subsequently, we produced a high-quality genome sequence of T. urartu using BAC-by-BAC sequencing strategy combining single molecule real-time sequencing and next-generation mapping technologies (Ling et al., 2018, Nature 557: 424-428). The assembled contig sequences were 4.79 Gb with an N50 of 344 kb and scaffold sequences were 4.86 Gb with an N50 of 3.67 Mb. With a high density single nucleotide polymorphism genetic map, 4.67 Gb (95.9%) of the scaffold sequences were successfully anchored on T. urartu chromosomes, constructing seven chromosome-scale pseudomolecules. By comparing collinear segments between T. urartu and its grass relatives, we proposed an evolution model of T. urartu chromosomes, and found that T. urtartu and Brachypodium were independently evolved from the grass ancestor with 12 chromosomes. Furthermore, we also found that the ancient genome duplications, which well maintained in rice, sorghum and Brachypodium, were strongly corrupted in T. urartu because of extensive amplifications of transposable elements and widespread gene loss.

In conclusion, we successfully generated a reference genome of the wheat A subgenome progenitor T. urartu. The assembly provides a valuable resource for studying genome evolution and genetic variation in wheat and related grasses, and promises to facilitate the discovery of genes that could be useful for wheat improvement.