Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

Jinfeng Chen, Quanfei Huang, Dongying Gao, Junyi Wang, Yongshan Lang, Tieyan Liu, Bo Li, Zetao Bai, Jose Luis Goicoechea, Chengzhi Liang, Chengbin Chen, Wenli Zhang, Shouhong Sun, Yi Liao, Xuemei Zhang, Lu Yang, Chengli Song, Meijiao Wang, Jinfeng Shi, Geng Liu, Junjie Liu, Heling Zhou, Weili Zhou, Qiulin Yu, Na An, Yan Chen, Qingle Cai, Bo Wang, Binghang Liu, Jiumeng Min, Ying Huang, Honglong Wu, Zhenyu Li, Yong Zhang, Ye Yin, Wenqin Song, Jiming Jiang, Scott A. Jackson, Rod A. Wing (), Jun Wang () and Mingsheng Chen ()
Additional contact information
Jinfeng Chen: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Quanfei Huang: BGI-Shenzhen
Dongying Gao: Institute of Plant Breeding, Genetics and Genomics, University of Georgia
Junyi Wang: BGI-Shenzhen
Yongshan Lang: BGI-Shenzhen
Tieyan Liu: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Bo Li: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Zetao Bai: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Jose Luis Goicoechea: Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona
Chengzhi Liang: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Chengbin Chen: Nankai University
Wenli Zhang: University of Wisconsin-Madison
Shouhong Sun: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Yi Liao: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Xuemei Zhang: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Lu Yang: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Chengli Song: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Meijiao Wang: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Jinfeng Shi: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Geng Liu: BGI-Shenzhen
Junjie Liu: BGI-Shenzhen
Heling Zhou: BGI-Shenzhen
Weili Zhou: BGI-Shenzhen
Qiulin Yu: BGI-Shenzhen
Na An: BGI-Shenzhen
Yan Chen: BGI-Shenzhen
Qingle Cai: BGI-Shenzhen
Bo Wang: BGI-Shenzhen
Binghang Liu: BGI-Shenzhen
Jiumeng Min: BGI-Shenzhen
Ying Huang: BGI-Shenzhen
Honglong Wu: BGI-Shenzhen
Zhenyu Li: BGI-Shenzhen
Yong Zhang: BGI-Shenzhen
Ye Yin: BGI-Shenzhen
Wenqin Song: Nankai University
Jiming Jiang: University of Wisconsin-Madison
Scott A. Jackson: Institute of Plant Breeding, Genetics and Genomics, University of Georgia
Rod A. Wing: Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona
Jun Wang: BGI-Shenzhen
Mingsheng Chen: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

Nature Communications, 2013, vol. 4, issue 1, 1-9

Abstract: Abstract The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.

Date: 2013
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DOI: 10.1038/ncomms2596

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