引用本文:	柳承璋,李富花,相建海.淡水枝角水蚤(Daphnia pulex)微小RNA(miRNA)的生物信息学发掘与分析.海洋与湖沼,2013,44(4):837-845.

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淡水枝角水蚤(Daphnia pulex)微小RNA(miRNA)的生物信息学发掘与分析
柳承璋¹, 李富花², 相建海²
1.中国科学院海洋研究所中国科学院大学;2.中国科学院海洋研究所

摘要:

微小RNA(microRNA或miRNA), 是广泛存在于多细胞生物及其病毒的一类由22个左右核苷酸组成的内源性非编码RNA, 具有转录后水平上的基因表达调控功能。本文在淡水枝角水蚤的全基因组序列的基础上, 通过生物信息学方法对淡水枝角水蚤(Daphnia pulex) miRNA进行了发掘, 得到miRNA前体(pre-miRNA) 252个、可编码262个功能miRNA; 发现了6个miRNA簇。8号染色体miRNA的出现频率显著高于其他染色体, 而4号染色体miRNA频率明显显著较低。通过与几种两侧对称动物的聚类分析将pre-miRNA归为191个miRNA家族, 其中105个家族为淡水枝角水蚤所特有, 15个家族为节肢动物门特有。在几种两侧对称动物中, 淡水枝角水蚤的miRNA与果蝇最为相似。

关键词: 淡水枝角水蚤甲壳动物 microRNA miRNA 微小RNA 生物信息学

DOI：10.11693/hyhz201304003003

分类号:

基金项目:国家自然科学基金重大项目, 30730071号; 国家863项目, 2012AA10A404号, 2012AA092205号

附件

Bioinformatic Analysis of Microrna Genes in Daphnia pulex

LIU Cheng-Zhang¹, LI Fu-Hua², XIANG Ji-Hai²

1.Institute of Oceanology, Chinese Academy of Sciences, University of Chinese Academy of Sciences;2.Institute of Oceanology, Chinese Academy of Sciences

Abstract:

MicroRNAs (miRNAs) are ~22nt long endogenous non-coding RNAs that regulate gene expression post-transcriptionally. Using a bioinformatic approach to analyze the whole genome sequence of Daphnia pulex, we predicted 252 pre-miRNAs which may produce 262 functional miRNAs, including 6 miRNA clusters. MiRNA occurrence frequency is significantly high on chromosome 8, while is significantly low on chromosome 4. Phlygenetic study of pre-miRNAs from 6 bilateria species was used to classify the D. pulex pre-miRNAs into 191 miRNA families, among which 105 are specific to D. pulex, while 15 are specific to Arthropoda. Among the compared bilateria species, D. pulex is most similar to Zebra fish in miRNA content.

Key words: Daphnia pulex crustacean microRNA miRNA bioinformatics