文章摘要
长牡蛎性腺中调控型非编码RNA的生物信息学分析
Bioinformatics Analysis of Regulatory Non-coding RNA in Gonad of Crassostrea gigas
投稿时间:2019-02-13  修订日期:2019-04-01
DOI:
中文关键词: 长牡蛎  微小RNA  长链非编码RNA  环状RNA  RNA-seq技术
英文关键词: Crassostrea gigas  miRNA  lncRNA  circRNA  RNA-seq
基金项目:国家自然科学基金
作者单位E-mail
王雪 上海海洋大学 wxwa1117@163.com 
王卫军 鲁东大学农学院 wwj2530616@163.com 
骆启豪 上海海洋大学  
孙国华 鲁东大学农学院  
冯艳微 鲁东大学农学院  
马敬俊 烟台市莱山区渔业海洋站  
杨建敏 鲁东大学农学院  
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中文摘要:
      本研究以日照海域同一家系的2龄长牡蛎(Crassostrea gigas)性腺为研究对象,通过small RNA-seq和RNA-seq技术筛选和鉴定出大量的miRNA、lncRNA、circRNA,并对其进行了生物学特征分析。研究结果表明,以斑马鱼(Danio rerio)为参考序列,获得25-30个已知miRNA成熟体和51-63个已知miRNA前体,预测到53-71个新 miRNA成熟体和53-77个新miRNA前体;长牡蛎miRNA长度分布介于18-26个核苷酸(nt)之间,其中分布在20-22 nt长度的miRNA数量最多,且miRNA首位碱基多为U。测序分析获得2302-2349个已知lncRNA转录本,预测到20083-24114个新lncRNA转录本,其中基因间型lncRNA(lincRNA)、内含子lncRNA(intronic lncRNA)、反义lncRNA(anti-sense lncRNA)分别占29.0%、62.1%和8.9%;长牡蛎lncRNA的基因组特征与其他真核生物的lncRNA基因组特征相似,与mRNA相比,exon个数少,转录本长度较短,表达水平低。测序分析共获得383个circRNA,其中平均88.54% circRNA来源于exon,平均4.51%来源于intronic,平均6.95%来源于intergenic,且鉴定出内源性circRNA潜在大量的miRNA结合位点。研究结果为后续研究长牡蛎调控型ncRNA的表达规律和生物学功能奠定了基础。
英文摘要:
      A plenty of non-coding RNAs (ncRNAs) have been identified through the application of high-throughput analysis of the transcriptome, and this has led to an intensive search for possible biological functions attributable to these transcripts. In this study, the gonad tissue of the two-year-age Crassostrea gigas of same family cultured in Rizhao Huanghai area were used to identify a large number of miRNA, lncRNA and circRNA by small RNA-seq and RNA-seq , and their biological characteristics were analyzed. The results showed that, with Danio rerio as a reference, 25-30 known miRNA matures and 51-63 known miRNA hairpin was obtained, 53-71 new miRNA matures and 53-77 new miRNA hairpin were predicted. The length of miRNA in C. gigas ranged from 18-26 nt, where the largest number was in the 20-22 nt and the first nucleotide position was tent to U. 2302-2349 known lncRNA transcripts were obtained, and 20083-24114 new lncRNA were predicted. Among them, the percentage of the intergenic lncRNA, intronic lncRNA and antisense lncRNA was 29.0%, 62.1%, and 8.9% , respectively. The data showed that genomic characteristics of lncRNA in C. gigas were similar to those of other eukaryotes. Compared with mRNA, the transcript and open reading frame of lncRNA was much shorter at length and much lower at expression level. 383 circRNA transcripts were obtained, among which the average percentage of 88.54% came from exon, 4.51% came from intronic and 6.95% came from intergenic. The data showed that the endogenous circRNA have a lot miRNA target sites. This study showed that the basic biological characteristics of miRNA, lncRNA and circRNA in C. gigas. The results set the foundation for the subsequent research on the expression and biological function of regulatory non-coding RNA in C. gigas.
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