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

Jingzhong Xie; Naxin Huo; Shenghui Zhou; Yi Wang; Guanghao Guo; Karin R. Deal; Shuhong Ouyang; Yong Liang; Zhenzhong Wang; Lichan Xiao; Tingting Zhu; Tiezhu Hu; Vijay Tiwari; Jianwei Zhang; Hongxia Li; Zhongfu Ni; Yingyin Yao; Huiru Peng; Shengli Zhang; Olin D. Anderson; Patrick E. McGuire; Jan Dvorak; Ming-Cheng Luo; Zhiyong Liu; Yong Q. Gu; Qixin Sun

doi:10.1016/j.jgg.2016.09.005

Volume 44 Issue 1

Jan. 2017

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

doi: 10.1016/j.jgg.2016.09.005

a
State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
b
USDA-ARS West Regional Research Center, Albany, CA 94710, USA
c
Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
d
Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
e
Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ 85721, USA

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Corresponding author: E-mail address: jdvorak@ucdavis.edu (Jan Dvorak); E-mail address: mcluo@ucdavis.edu (Ming-Cheng Luo); E-mail address: zyliu@genetics.ac.cn (Zhiyong Liu); E-mail address: yong.gu@ars.usda.gov (Yong Q. Gu); E-mail address: qxsun@cau.edu.cn (Qixin Sun)
Received Date: 2016-08-19
Accepted Date: 2016-09-27
Rev Recd Date: 2016-09-26

Available Online: 2016-10-05

Publish Date: 2017-01-20

Abstract

Abstract

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.
- Genome sequencing,
- Sequence assembly,
- Comparative genomics,
- Grass evolution

These authors contributed equally to this work.

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