|本期目录/Table of Contents|

[1]岳建宇,费忠安,郎小强,等.基于全基因组预测莱茵衣藻的新miRNA及其靶基因[J].应用与环境生物学报,2015,21(01):68-74.[doi:10.3724/SP.J.1145.2013.05021]
 YUE Jianyu,FEI Zhongan,LANG Xiaoqiang,et al.Genome-wide analysis of miRNAs and target prediction in Chlamydomonas reinhardtii[J].Chinese Journal of Applied & Environmental Biology,2015,21(01):68-74.[doi:10.3724/SP.J.1145.2013.05021]
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基于全基因组预测莱茵衣藻的新miRNA及其靶基因()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
21卷
期数:
2015年01期
页码:
68-74
栏目:
研究论文
出版日期:
2015-02-25

文章信息/Info

Title:
Genome-wide analysis of miRNAs and target prediction in Chlamydomonas reinhardtii
作者:
岳建宇 费忠安 郎小强 徐辉 乔代蓉 曹毅
四川大学生命科学学院生物信息与代谢工程共享实验平台 成都 610065
Author(s):
YUE Jianyu FEI Zhong’an LANG Xiaoqiang XU Hui QIAO Dairong CAO Yi
Sichuan Public Experimental Platform of Bioinformatics and Metabolic Engineering, College of Life Sciences, Sichuan University, Chengdu 610065, China
关键词:
莱茵衣藻miRNA全基因组比较基因组学同源比对靶基因生物信息学
Keywords:
Chlamydomonas reinhardtii miRNA comparative genomics homologous comparison genome-wide target gene bioinformatics
分类号:
Q811.4
DOI:
10.3724/SP.J.1145.2013.05021
文献标志码:
A
摘要:
莱茵衣藻(Chlamydomonas reinhardtii)是一种重要的模式生物,其miRNA的发现相对较晚. 为系统化地预测分析莱茵衣藻的miRNA,采用比较基因组和同源比对相结合的方法,根据miRbase中已知的莱茵衣藻miRNA序列以及前体的特点,并且基于莱茵衣藻的全基因组对其miRNA的前体序列和成熟miRNA进行系统的分析和筛选,使用unigene和JGI的莱茵衣藻相关序列数据库对预测结果进行靶基因预测和功能的分析. 最终发现可能存在的miRNA 36条,其前体结构符合miRNA前体的基本特征且具有高度的同源性,两个数据库所得相匹配靶基因分别为64和32条,其中部分是与莱茵衣藻各项生命活动相关的基因. 本研究表明莱茵衣藻的基因组中具有可能存在的新miRNA家族,并且部分有高度匹配的靶基因,为其后续研究提供了可靠的理论支持.
Abstract:
Chlamydomonas reinhardtii is an important model organism, but its miRNA is not fully understood. Therefore, systemic prediction and analysis of Chlamydomonas reinhardtii miRNA is of important significance for further researches. This study aimed to set up the parameters including GC content of pre-miRNA, number of loops in pre-miRNA secondary structure, size of loop, folding free energy and minimal folding free energy index, using the genome and homologous alignment method in combination with the characteristics of known 85 miRNA sequences and precursors of Chlamydomonas reinhardtii in miRbase. Based on the whole genome, the miRNA precursor sequences and mature miRNA were systemically analyzed and screened. Finally the softwares psRNATarget and psRobot were used based on the sequence data of Chlamydomonas reinhardtii from the unigene and JGI genomic databases to conduct target gene prediction and functional analysis of prediction results. All together 36 possible miRNAs were defined, with the two softwares obtaining 64 and 32 matched target genes respectively. The result indicated probable existence of a new miRNA family with some highly matched target genes in Chlamydomonas reinhardtii genome .

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备注/Memo

备注/Memo:
国家自然科学基金项目(31272659,31171447,30971817)、国家“十二五”科技支撑计划项目(2014BAD02B02,2013BAD10B01)和国家科技基础条件平台项目(NIMR-2014-8)资助 Supported by the National Natural Science Foundation of China (31272659, 31171447, 30971817), the Sci-tech Pillar Project of the Twelfth Five-year Plan of China (2014BAD02B02, 2013BAD10B01), and the National Sci-tech Infrastructure and Facility Development Program of China (NIMR-2014-8)
更新日期/Last Update: 2015-02-15