Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

Jizeng Jia, Shancen Zhao, Xiuying Kong, Yingrui Li, Guangyao Zhao, Weiming He, Rudi Appels, Matthias Pfeifer, Yong Tao, Xueyong Zhang, Ruilian Jing, Chi Zhang, Youzhi Ma, Lifeng Gao, Chuan Gao, Manuel Spannagl, Klaus F. X. Mayer, Dong Li, Shengkai Pan, Fengya Zheng, Qun Hu, Xianchun Xia, Jianwen Li, Qinsi Liang, Jie Chen, Thomas Wicker, Caiyun Gou, Hanhui Kuang, Genyun He, Yadan Luo, Beat Keller, Qiuju Xia, Peng Lu, Junyi Wang, Hongfeng Zou, Rongzhi Zhang, Junyang Xu, Jinlong Gao, Christopher Middleton, Zhiwu Quan, Guangming Liu, Jian Wang, Huanming Yang, Xu Liu, Zhonghu He, Long Mao, Jun Wang

About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD). Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker's flour. Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.