稻屬是從事植物比較、進(jìn)化和功能基因組學(xué)研究的理想系統(tǒng),。野生稻蘊(yùn)含著寶貴的基因資源,。為了更好地利用稻屬的野生資源，美國(guó)亞利桑那大學(xué)的Rod Wing教授在2009年發(fā)起了國(guó)際稻屬基因組計(jì)劃（I-OMAP）,，旨在構(gòu)建稻屬所有物種的全基因組序列圖譜,，并在此基礎(chǔ)上開(kāi)展比較、進(jìn)化和功能基因組學(xué)研究,。
在I-OMAP計(jì)劃的框架下,，中國(guó)科學(xué)院遺傳與發(fā)育生物學(xué)研究所陳明生課題組通過(guò)與深圳華大基因、亞利桑那大學(xué)等合作,，利用第二代測(cè)序技術(shù)完成了261 Mb高質(zhì)量的短花藥野生稻（O. brachyantha）全基因組序列,，并開(kāi)展了稻屬比較基因組學(xué)和基因組進(jìn)化的研究。研究揭示了稻屬基因組在基因組大小,、基因移動(dòng)和異染色質(zhì)進(jìn)化等方面新的分子機(jī)制,。
該研究于3月12日在線發(fā)表于Nature Communications。陳金鋒博士為該論文的第一作者,。參與該研究的合作者包括深圳華大基因,、亞利桑那大學(xué)基因組研究所（Rod Wing教授等）,、喬治亞大學(xué)（Scott Jackson教授和Dongying Gao博士）,、University of Wisconsin-Madison（Jiming Jiang教授和Wenli Zhang博士）,、南開(kāi)大學(xué)（宋文芹教授和陳成彬博士）和中科院遺傳發(fā)育所基因組分析平臺(tái)（梁承志研究員）等,。
該研究得到了國(guó)家自然科學(xué)基金委重大國(guó)際合作研究項(xiàng)目和植物基因組學(xué)國(guó)家重點(diǎn)實(shí)驗(yàn)室自主研究課題的資助,。(生物谷Bioon.com）
doi:10.1038/ncomms2596
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PMID:
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
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.
