娄素琳,朱秀兰,曾志勇,等.盐藻microRNAs高通量测序和生物信息学分析[J].深圳大学学报理工版,2018,35(No.4(331-440)):331-333.[doi:10.3724/SP.J.1249.2018.04331]
LOU Sulin,ZHU Xiulan,ZENG Zhiyong,et al.Bioinformatics analysis of Dunaliella microRNAs by high-throughput sequencing[J].Journal of Shenzhen University Science and Engineering,2018,35(No.4(331-440)):331-333.[doi:10.3724/SP.J.1249.2018.04331]
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盐藻microRNAs高通量测序和生物信息学分析
娄素琳1,2,3,朱秀兰1,3,曾志勇1,3,李 辉1,3,4,胡章立1,3,4

1)深圳大学生命与海洋科学学院,深圳市海洋生物资源与生态环境重点实验室,广东深圳 518060; 2)深圳大学 光电工程学院,光电子器件与系统教育部/广东省重点实验室,广东深圳 518060; 3)广东省植物表观遗传学重点实验室, 广东深圳 518060; 4)深圳大学龙华生物产业创新研究院,深圳市海洋藻类生物工程技术研究中心,广东深圳 518060

分子生物学; 生物信息学; 高通量测序; 杜氏盐藻; 小核糖核酸; β-胡萝卜素

Bioinformatics analysis of Dunaliella microRNAs by high-throughput sequencing
LOU Sulin1,2,3, ZHU Xiulan1,3, ZENG Zhiyong1,3, LI Hui1,3,4, and HU Zhangli1,3,4

1)College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, Shenzhen University, Shenzhen 518060, Guangdong Province, P.R.China2)College of Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, Guangdong Province, P.R.China3)Guangdong Key Laboratory of Plant Epigenetics, Shenzhen 518060, Guangdong Province, P.R.China4)Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, Guangdong Province, P.R.China

molecular biology; bioinformatics; high-throughput sequencing; Dunaliella salina; microRNAs; beta-carotene

DOI: 10.3724/SP.J.1249.2018.04331

备注

小核糖核酸(micro ribonucleic acid, microRNA 或miRNA)是一类内源性长约21～24个核苷酸碱基(nucleotide, nt)的非编码RNA,在真核生物的基因转录后调控中起着重要作用.杜氏盐藻(Dunaliella salina)是β-胡萝卜素含量最高的真核微藻,为探究其是否存在内源miRNA,构建了小RNA文库,通过Illumina HiSeqTM2500高通量测序的方法对盐藻进行小RNA测序.测序共获得11 542 169条clean tags(3个盐藻文库clean tags数的平均值).比对GnenBank数据库、Rfam数据库及盐藻的参考基因组数据,筛选后的clean tags数据再比对miRBase数据库,3个盐藻生物学重复分别获得已知miRNA为42、41和44个.比对盐藻参考基因组及其miRNA前体发卡结构预测,3个重复分别获得盐藻新的miRNA 为920、880和957个.预测所有miRNA的靶基因,并对其进行功能富集,发现靶基因在细胞代谢进程、分子功能的结合和催化活性方面较多.首次鉴定了杜氏盐藻中具有miRNA的存在,对揭示miRNA这一调控机制广泛存在于单细胞真核绿藻提供了依据.

Micro ribonucleic acid(microRNA / miRNA)is a class of endogenous non-coding RNA with a length of about 21-24 nt, which plays important roles in the post-transcriptional regulation of eukaryotes. Dunaliella salina is a eukaryotic green alga with high content of beta-carotene. To investigate the presence of miRNA, small RNA libraries of Dunaliella are built for sequencing by Illumina HiSeqTM2500 high-throughput sequencing method. A total of 11 542 169 clean tags(average number of clean tags in three Dunaliella small RNA libraries)are gained. Aligned with GnenBank database, Rfam database and the reference genome data of Dunaliella, the screened of the clean tags are then searched against miRBase database, and 42, 41 and 44 known miRNAs are identified from three biological replicates. According to the reference genome and the hairpin structure prediction of miRNA precursor, 920, 880 and 957 novel miRNAs are obtained. The target genes of all the miRNAs are predicted, and the function enrichment analysis of target genes shows that there are abundant in cellular process, binding and catalytic activity of molecular function. This is the first time to identify the presence of miRNA in Dunaliella. It reveals that the miRNA regulation mechanism is general in unicellular eukaryotic microalgae.

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