长白落叶松小RNA测序和其靶基因预测

张素芳; 张磊; 赵佳丽; 张莉; 张含国

doi:10.13332/j.1000-1522.20150404

长白落叶松小RNA测序和其靶基因预测

东北林业大学林木遗传育种国家重点实验室

基金项目:

“863”国家高技术研究发展计划项目(2013AA102704)、中央高校基本科研业务费专项(2572016CA08、2572016AA36)。

详细信息

作者简介:
张素芳,博士生。主要研究方向:林木遗传改良。Email:171998329@qq.com 地址:150040黑龙江省哈尔滨市香坊区和兴路26号东北林业大学林学院。
责任作者: 张含国,教授,博士生导师。主要研究方向:林木遗传改良。Email:hanguozhang1@sina.com 地址:同上。

张素芳,博士生。主要研究方向:林木遗传改良。Email:171998329@qq.com 地址:150040黑龙江省哈尔滨市香坊区和兴路26号东北林业大学林学院。
责任作者: 张含国,教授,博士生导师。主要研究方向:林木遗传改良。Email:hanguozhang1@sina.com 地址:同上。

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出版历程
- 收稿日期: 2015-12-18
- 发布日期: 2016-12-30

Small RNA sequencing and target gene prediction in Larix olgensis.

State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, P. R. China.

摘要

摘要: miRNA是近年来新发现的一种比较特殊的具有高度保守的小RNA,其在基因调控网络中扮演着重要的角色。本文借助Illumia测序平台,经过Solexa测序分析,对长白落叶松的miRNA进行了分析,最终筛选出了15 294 797条clean reads。比对结果显示,除去核糖体RNA(rRNA)2 991 972条、转运RNA(tRNA)65 264条、核内小RNA(snRNA)1 670条、核仁小RNA(snoRNA)467条等ncRNA以及重复序列6 421条,共获得未获得注释的miRNA 12 229 003条,占总注释小RNA的79.96%。利用miRDeep2对未注释的小RNA进行miRNA的筛选,共得到78个新发现的miRNA,分别隶属于miR164、miR166、miR160、miR950、miR396家族。通过进一步对靶基因的注释分析共得到333个与其相对应的靶基因;其功能包括转录因子类,未知功能蛋白,离子结合蛋白,延长因子,信号转导,细胞壁或细胞膜的生物合成等调控植物生长发育过程。
- 小RNA /
- 长白落叶松 /
- miRNA /
- 靶基因
Abstract: miRNA is a relatively special and highly conserved RNA, which plays an important role in gene regulation network. In this study, with the help of Illumia sequencing platform and the Solexa sequencing analysis of miRNA in Larix olgensis, we ultimately selected 15 294 797 clean reads, in which rRNA is 2 991 972 reads, tRNA 65 264 reads, snRNA 1 670 reads and snoRNA 467 reads, and ncRNAs and repeat sequences contain 6 421 reads. Un-annotated miRNA has 12 229 003 reads, accounting for 79.96% of the total RNA notes. The miRDeep2 was used to screen the miRNA, and 78 new miRNAs were obtained overall, which belong to the miR164, miR166, miR950, miR160, and miR396 families. Through further analysis of the target gene notes, we obtained 333 corresponding target genes, and their functions include transcription factors, unknown functional proteins, binding proteins, elongation factors, signal transduction, cell wall and cell membrane biosynthesis involved in regulation of plant growth and development process.
- sRNA /
- Larix olgensis /
- miRNA /
- target gene

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