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

被引：155

作者：

Chen, Jinfeng ^{[1
]}

Huang, Quanfei ^{[2
]}

Gao, Dongying ^{[3
]}

Wang, Junyi ^{[2
]}

Lang, Yongshan ^{[2
]}

Liu, Tieyan ^{[1
]}

Li, Bo ^{[1
]}

Bai, Zetao ^{[1
]}

Goicoechea, Jose Luis ^{[4
]}

Liang, Chengzhi ^{[1
]}

Chen, Chengbin ^{[5
]}

Zhang, Wenli ^{[6
]}

Sun, Shouhong ^{[1
]}

Liao, Yi ^{[1
]}

Zhang, Xuemei ^{[1
]}

Yang, Lu ^{[1
]}

Song, Chengli ^{[1
]}

Wang, Meijiao ^{[1
]}

Shi, Jinfeng ^{[1
]}

Liu, Geng ^{[2
]}

Liu, Junjie ^{[2
]}

Zhou, Heling ^{[2
]}

Zhou, Weili ^{[2
]}

Yu, Qiulin ^{[2
]}

An, Na ^{[2
]}

Chen, Yan ^{[2
]}

Cai, Qingle ^{[2
]}

Wang, Bo ^{[2
]}

Liu, Binghang ^{[2
]}

Min, Jiumeng ^{[2
]}

Huang, Ying ^{[2
]}

Wu, Honglong ^{[2
]}

Li, Zhenyu ^{[2
]}

Zhang, Yong ^{[2
]}

Yin, Ye ^{[2
]}

Song, Wenqin ^{[5
]}

Jiang, Jiming ^{[6
]}

Jackson, Scott A. ^{[3
]}

Wing, Rod A. ^{[4
]}

Wang, Jun ^{[2
,7
,8
]}

Chen, Mingsheng ^{[1
]}

机构：

[1] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Gen, Beijing 100101, Peoples R China

[2] Beishan Ind Zone, BGI Shenzhen, Shenzhen 518083, Peoples R China

[3] Univ Georgia, Inst Plant Breeding Genet & Genom, Athens, GA 30602 USA

[4] Univ Arizona, Sch Plant Sci, BIO5 Inst, Genom Inst, Tucson, AZ 85721 USA

[5] Nankai Univ, Dept Genet & Cell Biol, Tianjin 300071, Peoples R China

[6] Univ Wisconsin, Dept Hort, Madison, WI 53706 USA

[7] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

[8] King Abdulaziz Univ, Jeddah 21589, Saudi Arabia

来源：

NATURE COMMUNICATIONS | 2013年 / 4卷

基金：

美国国家科学基金会; 中国国家自然科学基金;

关键词：

RECIPROCAL GENE LOSS; TRANSPOSABLE ELEMENTS; RICE; DNA; DIVERSIFICATION; RECOMBINATION; REARRANGEMENT; CONSTRUCTION; MICROSYNTENY; DIVERGENCE;

D O I：

10.1038/ncomms2596

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：9

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