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

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

J Genet Genomics. 2017 Jan 20;44(1):51-61. doi: 10.1016/j.jgg.2016.09.005. Epub 2016 Oct 5.

Authors

Jingzhong Xie¹, Naxin Huo², Shenghui Zhou¹, Yi Wang³, Guanghao Guo¹, Karin R Deal⁴, Shuhong Ouyang¹, Yong Liang¹, Zhenzhong Wang¹, Lichan Xiao⁴, Tingting Zhu⁴, Tiezhu Hu³, Vijay Tiwari⁵, Jianwei Zhang⁶, Hongxia Li³, Zhongfu Ni¹, Yingyin Yao¹, Huiru Peng¹, Shengli Zhang³, Olin D Anderson³, Patrick E McGuire⁴, Jan Dvorak⁷, Ming-Cheng Luo⁸, Zhiyong Liu⁹, Yong Q Gu¹⁰, Qixin Sun¹¹

Affiliations

¹ State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
² USDA-ARS West Regional Research Center, Albany, CA 94710, USA; Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
³ USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
⁴ Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
⁵ Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
⁶ Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ 85721, USA.
⁷ Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA. Electronic address: [email protected].
⁸ Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA. Electronic address: [email protected].
⁹ State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: [email protected].
¹⁰ USDA-ARS West Regional Research Center, Albany, CA 94710, USA. Electronic address: [email protected].
¹¹ State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: [email protected].

PMID: 27765484
DOI: 10.1016/j.jgg.2016.09.005

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.

Keywords: Aegilops tauschii; Comparative genomics; Genome sequencing; Grass evolution; Sequence assembly.

Publication types

Comparative Study
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Chromosomes, Plant / genetics*
Evolution, Molecular*
Genome, Plant / genetics*
INDEL Mutation
Poaceae / genetics*
Polymorphism, Single Nucleotide
Sequence Analysis*
Synteny
Triticum / genetics*