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. AndersonPatrick E. McGuire, Jan Dvorak, Ming Cheng Luo, Zhiyong Liu, Yong Q. Gu, Qixin Sun

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)51-61
Number of pages11
JournalJournal of Genetics and Genomics
Volume44
Issue number1
DOIs
StatePublished - Jan 20 2017

Fingerprint

Triticum
Chromosomes
Genome
Polyploidy
Brachypodium
Genes
DNA Transposable Elements
Chromosomes, Human, Pair 3
Sorghum
Bread
Poaceae
Diploidy
Clone Cells
Technology
Proteins

Keywords

  • Aegilops tauschii
  • Comparative genomics
  • Genome sequencing
  • Grass evolution
  • Sequence assembly

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes. / Xie, Jingzhong; Huo, Naxin; Zhou, Shenghui; Wang, Yi; Guo, Guanghao; Deal, Karin R.; Ouyang, Shuhong; Liang, Yong; Wang, Zhenzhong; Xiao, Lichan; Zhu, Tingting; Hu, Tiezhu; Tiwari, Vijay; Zhang, Jianwei -; Li, Hongxia; Ni, Zhongfu; Yao, Yingyin; Peng, Huiru; Zhang, Shengli; Anderson, Olin D.; McGuire, Patrick E.; Dvorak, Jan; Luo, Ming Cheng; Liu, Zhiyong; Gu, Yong Q.; Sun, Qixin.

In: Journal of Genetics and Genomics, Vol. 44, No. 1, 20.01.2017, p. 51-61.

Research output: Contribution to journalArticle

Xie, J, Huo, N, Zhou, S, Wang, Y, Guo, G, Deal, KR, Ouyang, S, Liang, Y, Wang, Z, Xiao, L, Zhu, T, Hu, T, Tiwari, V, Zhang, J, Li, H, Ni, Z, Yao, Y, Peng, H, Zhang, S, Anderson, OD, McGuire, PE, Dvorak, J, Luo, MC, Liu, Z, Gu, YQ & Sun, Q 2017, 'Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes', Journal of Genetics and Genomics, vol. 44, no. 1, pp. 51-61. https://doi.org/10.1016/j.jgg.2016.09.005
Xie, Jingzhong ; Huo, Naxin ; Zhou, Shenghui ; Wang, Yi ; Guo, Guanghao ; Deal, Karin R. ; Ouyang, Shuhong ; Liang, Yong ; Wang, Zhenzhong ; Xiao, Lichan ; Zhu, Tingting ; Hu, Tiezhu ; Tiwari, Vijay ; Zhang, Jianwei - ; Li, Hongxia ; Ni, Zhongfu ; Yao, Yingyin ; Peng, Huiru ; Zhang, Shengli ; Anderson, Olin D. ; McGuire, Patrick E. ; Dvorak, Jan ; Luo, Ming Cheng ; Liu, Zhiyong ; Gu, Yong Q. ; Sun, Qixin. / Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes. In: Journal of Genetics and Genomics. 2017 ; Vol. 44, No. 1. pp. 51-61.
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AU - Zhou, Shenghui

AU - Wang, Yi

AU - Guo, Guanghao

AU - Deal, Karin R.

AU - Ouyang, Shuhong

AU - Liang, Yong

AU - Wang, Zhenzhong

AU - Xiao, Lichan

AU - Zhu, Tingting

AU - Hu, Tiezhu

AU - Tiwari, Vijay

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AU - Li, Hongxia

AU - Ni, Zhongfu

AU - Yao, Yingyin

AU - Peng, Huiru

AU - Zhang, Shengli

AU - Anderson, Olin D.

AU - McGuire, Patrick E.

AU - Dvorak, Jan

AU - Luo, Ming Cheng

AU - Liu, Zhiyong

AU - Gu, Yong Q.

AU - Sun, Qixin

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