Qi Pengzhi, Guo Baoying, Zhu Aiyi, Wu Changwen, Liu Changlin
National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China.
National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China.
Fish Shellfish Immunol. 2014 Aug;39(2):483-91. doi: 10.1016/j.fsi.2014.06.009. Epub 2014 Jun 17.
Two sRNA libraries with or without poly(I:C) infection of large yellow croaker Pseudosciaena crocea were constructed and sequenced using the high-throughput Illumina/Solexa deep sequencing technology. The high-throughput sequencing pipeline yielded 163,79,272 and 217,07,070 raw reads corresponding to 132,27,594 and 206,86,409 clean reads for the normal and infected libraries, respectively. Bioinfromatic analysis identified 534 miRNAs, of which, 158 miRNAs were known in miRBase 20.0 and the remaining 376 were not found homology to any known metazoan miRNAs, suggesting a possible species-specificity. We analyzed the significance of differently expressed miRNAs between two libraries using pairwise comparison. There was significant differential expression of 112 miRNAs (p < 0.001) between two libraries. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR experiments (RT-qPCR) were preformed for 6 miRNAs of the two samples, and agreement was found between the sequencing and RT-qPCR data. To our knowledge, this is the first comprehensive study of miRNAs in P. crocea and of expression analysis of P. crocea miRNAs in response to poly(I:C) infection, and many miRNAs were differentially regulated under normal and infection conditions. These findings deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various foreign infection in P. crocea.
构建了大黄鱼（Pseudosciaena crocea）在有无聚肌胞苷酸（poly(I:C)）感染情况下的两个小RNA文库，并使用高通量Illumina/Solexa深度测序技术进行测序。高通量测序流程分别为正常文库和感染文库产生了163,79,272条和217,07,070条原始读数，对应132,27,594条和206,86,409条clean reads。生物信息学分析鉴定出534个微小RNA（miRNA），其中158个miRNA在miRBase 20.0中是已知的，其余376个未发现与任何已知后生动物miRNA具有同源性，表明可能存在物种特异性。我们通过成对比较分析了两个文库之间差异表达miRNA的显著性。两个文库之间有112个miRNA存在显著差异表达（p < 0.001）。其中，鉴定出一些已知的与免疫相关的miRNA。对两个样本中的6个miRNA进行了实时定量PCR实验（RT-qPCR），测序数据和RT-qPCR数据之间具有一致性。据我们所知，这是首次对大黄鱼miRNA进行全面研究以及对大黄鱼miRNA在聚肌胞苷酸（poly(I:C)）感染应答中的表达分析，并且许多miRNA在正常和感染条件下受到差异调节。这些发现加深了我们对miRNA在复杂宿主免疫系统中作用的理解，并且对于开发针对大黄鱼宿主免疫防御各种外来感染的新控制策略应该是有用的。
