Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes

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• 作者：Jingzhong Xie^a ; ¹ ; Naxin Huo^b ; ^c ; ¹ ; Shenghui Zhou^a ; ¹ ; Yi Wang^b ; ¹ ; Guanghao Guo^a ; Karin R. Deal^c ; Shuhong Ouyang^a ; Yong Liang^a ; Zhenzhong Wang^a ; Lichan Xiao^c ; Tingting Zhu^c ; Tiezhu Hu^b ; Vijay Tiwari^d ; Jianwei Zhang^e ; Hongxia Li^b ; Zhongfu Ni^a ; Yingyin Yao^a ; Huiru Peng^a ; Shengli Zhang^b ; Olin D. Anderson^b ; Patrick E. McGuire^c ; Jan Dvorak^c ; ^{jdvorak@ucdavis.edu} ; Ming-Cheng Luo^c ; ^{mcluo@ucdavis.edu} ; Zhiyong Liu^a ; ^{zyliu@genetics.ac.cn} ; Yong Q. Gu^b ; ^{yong.gu@ars.usda.gov} ; Qixin Sun^a ; ^{qxsun@cau.edu.cn}
• 关键词：Aegilops tauschii ; Genome sequencing ; Sequence assembly ; Comparative genomics ; Grass evolution
• 刊名：Journal of Genetics and Genomics
• 出版年：2017
• 出版时间：20 January 2017
• 年：2017
• 卷：44
• 期：1
• 页码：51-61
• 全文大小：3453 K
• 卷排序：44

文摘

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 a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, 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 Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. 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 At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.