Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication

文献类型： 外文期刊

第一作者： Wang, Yu

作者： Wang, Yu;Bai, Xuefei;Yan, Chenghai;Gui, Yiejie;Fan, Longjiang;Wang, Yu;Bai, Xuefei;Yan, Chenghai;Gui, Yiejie;Fan, Longjiang;Wei, Xinghua;Guo, Longbiao;Zhu, Qian-Hao

作者机构：

关键词： degradome;genome;MIRNA;Oryza rufipogon;rice domestication

期刊名称：NEW PHYTOLOGIST （ 影响因子：10.151； 五年影响因子：10.475 ）

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收录情况： SCI

摘要： The lackof aMIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and adegradomeof O. rufipogon were sequencedby lllumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips. A de novo O. rufipogon genome was assembled using c. 55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogongenome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be atarget of domestication, as demonstrated for the miR164 family. Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication.

分类号： Q94

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