Bread wheat(Triticum aestivum,AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations.A high-quality genome sequence assembly of diploid Aegilops tauschii,the donor of the wheat D genome,will provide a useful platform to study polyploid wheat evolution.A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path(MTP) of 3176 BAC clones from the short arm of Ae.tauschii chromosome 3(At3DS).The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes.Compared with the orthologous regions of rice,Brachypodium,and sorghum,At3 DS contains 38.67%more genes.In comparison to At3 DS,the short arm sequence of wheat chromosome 3B(Ta3BS) is 95-Mb large in size,which is primarily due to the expansion of the non-centromeric region,suggesting that transposable element(TE) bursts in Ta3 B likely occurred there.Also,the size increase is accompanied by a proportional increase in gene number in Ta3 BS.We found that in the sequence of short arm of wheat chromosome 3D(Ta3DS),there was only less than 0.27%gene loss compared to At3 DS.Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome. Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution . A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. Tuschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3 DS contains 38.67% more genes. In comparison to At3 DS, the short arm sequence of wheat chromosome 3B (Ta3BS) is 95-Mb large in size, which is in due to the expansion of the non-centromeric region, suggesting that transposable element (TE) bursts in Ta3 B likely occurred the re.Also, the size increase is accompanied by a proportional increase in gene number in Ta3 BS.We found that in the sequence of short arm of wheat chromosome 3D (Ta3DS), there was only less than 0.27% gene loss compared to At3 DS . Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.