doi:

DOI: 10.3724/SP.J.1249.2018.04331

Journal of Shenzhen University Science and Engineering (深圳大学学报理工版) 2018/35:4 PP.331-333

Bioinformatics analysis of Dunaliella microRNAs by high-throughput sequencing


Abstract:
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.

Key words:molecular biology,bioinformatics,high-throughput sequencing,Dunaliella salina,microRNAs,beta-carotene

ReleaseDate:2018-07-26 10:51:01



[1] VARELA J C, PEREIRA H, VILA M,et al. Erratun to:production of carotenoids by microalgae:achievements and challenges[J]. Photosynthesis Research,2016,127(3):285-286.

[2] POLLE JEW, BARRY K, CUSHMAN J, et al. Draft nuclear genome sequence of the halophilic and beta-carotene accumulating green alga Dunaliella salina strain CCAP19/18[J]. Genome Announcements, 2017, 5:1105-1117.

[3] LEE R C, FEINBAUM R L, AMBROS V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14[J]. Cell, 1993, 75(5):843-854.

[4] ZHAO Tao, LI Guanglin, MI Shijun,et al. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii[J]. Genes & Development, 2007,21(10):1190-1203.

[5] MOLNÁR A, SCHWACH F, STUDHOLME D J,et al. MiRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii[J]. Nature,2007,447(7148):1126-1129.

[6] 胡章立,舒龙飞,苟德明.莱茵衣藻硫胁迫相关microRNA检测及其靶基因分析[J].深圳大学学报理工版,2011,28(6):237-242. HU Zhangli,SHU Longfei,GOU Deming.MicroRNAs quantification and related target genes for response to sulfur deprivation in Chlamydomonas reinhardtii[J].Journal of Shenzhen University Science and Engineering, 2011,28(6):237-242.(in Chinese)

[7] LI Jingrui, WU Yang, QI Yijun. MicroRNAs in a multicellular green alga volvox carteri[J].Science China:Life Sciences, 2014,57(1):36-45.

[8] YAMASAKI T, VOSHALL A, KIM E J, et al. Complementarity to an miRNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green alga Chlamydomonas reinhardtii[J]. Plant Journal for Cell & Molecular Biology, 2013, 76(6):1045-1056.