利用深度测序技术检测玉米根系和叶片中已知的microRNAs

doi:10.3724/SP.J.1005.2010.01175

遗传 ›› 2010, Vol. 32 ›› Issue (11): 1175-1186.doi: 10.3724/SP.J.1005.2010.01175

利用深度测序技术检测玉米根系和叶片中已知的microRNAs

陈洁^{1, 2}, 林海建¹, 潘光堂¹, 张志明¹, 张彪², 沈亚欧¹, 覃成¹, 张谦³, 赵茂俊⁴

1. 四川农业大学玉米研究所, 教育部作物基因资源与遗传改良重点实验室, 雅安 625014; 2. 四川省农业科学院作物研究所, 国家玉米改良分中心, 成都 610066; 3. 四川省农业科学院农产品加工研究所, 成都 610066; 4. 四川农业大学生命科学与理学院, 雅安 625014

收稿日期:2010-04-24 修回日期:2010-06-29 出版日期:2010-11-20 发布日期:2010-11-25
通讯作者: 潘光堂 E-mail:pangt1956@yahoo.com.cn
基金资助:
国家自然科学基金项目(编号：30900901)和转基因生物新品种培育重大专项(编号：2008ZX08003-003)资助

Identification of known microRNAs in root and leaf of maize by deep sequencing

CHEN Jie^{1, 2}, LIN Hai-Jian¹, PAN Guang-Tang¹, ZHANG Zhi-Ming¹, ZHANG Biao², SHEN Ya-Ou¹, QIN Cheng¹, ZHANG Qian³, ZHAO Mao-Jun⁴

1. Maize Research Institute, Sichuan Agricultural University, Ya’an 625014, China;
2. Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
3. Institute of Agricultural Products Processing, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
4. Life and Science Department, Sichuan Agricultural University, Ya’an 625014, China

Received:2010-04-24 Revised:2010-06-29 Online:2010-11-20 Published:2010-11-25
Contact: PAN Guang-Tang E-mail:pangt1956@yahoo.com.cn

摘要/Abstract

摘要： microRNA (miRNA)是一类具有20~24 nt 核苷酸长度的非蛋白质编码的内源小分子RNA, 它在植物生长发育和逆境胁迫响应等过程中发挥着重要作用。文章利用基于Illumina/Solexa原理的小分子RNA深度测序技术, 结合生物信息学的方法对玉米根系和叶片中已知miRNA的类型、丰度及靶基因进行了分析。研究发现, 在根系中共检测到92个已知的miRNA, 分别属于18个miRNA家族, 其表达丰度在1~105 943之间; 在叶片中, 共发现86个已知的miRNA, 分别属于17个miRNA家族, 其表达丰度在1~85 973之间。靶基因预测结果表明, 根系中的18个miRNA家族共靶向54个蛋白, 进一步的功能预测发现, 这些基因涉及了转录调控、物质能量代谢、电子传递、胁迫响应和信号转导等过程。以上研究结果表明, 就已知的miRNA而言, 无论是miRNA的类型还是表达丰度, 在玉米根系和叶片中都存在较大差异。

关键词: microRNA, 深度测序, 丰度分析, 靶基因预测, 玉米

Abstract: microRNA (miRNAs) is a newly identified class of 20~24 nt non-protein-coding and endogenous small RNA, which plays an important role in plant growth, development and response to environmental stresses. Combined with bioinformatic method, the types, abundance, and targets of known miRNAs in root and leaf of maize (Zea mays L.) were analyzed by small RNA deep sequencing technology, which was based on Illumina/Solexa principium. The results indicated that 92 known miRNAs were detected in maize root, which were attributed to 18 miRNA families and their abundance ranged from 1 to 105 943 reads. Synchronously, 86 known miRNAs were detected in maize leaf, which were attributed to 17 miRNA families and their abundance ranged from 1 to 85 973 reads. The target gene prediction showed that 54 putative target genes as these known miRNAs were predicted. Some of them were involved in the following processes, such as tran-scription regulation, substance and energy metabolism, electron transport, stress response, and signal transduction through further function prediction. In conclusion, there were obvious differences in both types and abundance of known miRNAs between root and leaf in maize.

Key words: Maize, microRNA, Deep sequencing, Abundance analysis, Target prediction

陈洁，林海建，潘光堂，张志明，张彪，沈亚欧，覃成，张谦，赵茂俊. 利用深度测序技术检测玉米根系和叶片中已知的microRNAs[J]. 遗传, 2010, 32(11): 1175-1186.

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利用深度测序技术检测玉米根系和叶片中已知的microRNAs

Identification of known microRNAs in root and leaf of maize by deep sequencing

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