De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure
De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure
复制标题
标枪虾虎鱼 Synechogobius hasta 肝脏转录组的从头表征及其水性铜暴露后的转录组谱分析
DOI：
10.1007/s10695-015-0190-2
复制
发表时间：
2016-06-01
影响因子：
2.9
通讯作者：
Wu, Kun
中科院分区：
文献类型：
--
作者：
Chen, Qi-Liang;Luo, Zhi;Wu, Kun
先前的研究已经研究了长尾鱼肝脏对铜（Cu）暴露的生理反应；然而，关于潜在的分子机制的信息很少。为了更好地了解铜中毒的机制，阐明铜暴露调控的全局基因表达模式，我们利用RNA测序（RNA-seq）技术获得了海丝桃肝脏转录组信息，并研究了水源铜暴露后基因的差异表达。利用Illumina测序平台，共生成60,217个unigene，过滤组装后平均长度为815 bp， unigene N50长度为1298 bp。在功能注释分析中，分别有34,860、31,526、31,576、25,808、11,542和21,721个unique被注释到NR、NT、Swiss-Prot、KEGG、COG和GO数据库中，总共有37,764个unique被注释。55 μg Cu/l处理30 d后，共有292个基因显著上调，1076个基因显著下调。通过KEGG分析，660具有特定的通路注释。随后的生物信息学分析显示，差异表达基因主要与脂质代谢、免疫系统、细胞凋亡和信号转导有关，提示这些信号通路可能受到Cu暴露的调节。本研究为后续海丝藻基因表达研究提供了全面的序列信息，Cu暴露后的转录组分析也有望提高我们对Cu分子毒理学的理解。
Previous studies have investigated the physiological responses to chronic copper (Cu) exposure in the liver of Synechogobius hasta; however, little information is available on the underlying molecular mechanisms. In an effort to better understand the mechanisms of Cu toxicity and to illuminate global gene expression patterns modulated by Cu exposure, we obtained the liver transcriptome information of S. hasta by RNA sequencing (RNA-seq) technology and also investigated the differential expression of genes following waterborne Cu exposure. Using the Illumina sequencing platform, as many as 60,217 unigenes were generated, with 815 bp of average length and 1298 bp of unigene N50 after filtering and assembly. For functional annotation analysis, 34,860, 31,526, 31,576, 25,808, 11,542, and 21,721 unigenes were annotated to the NR, NT, Swiss-Prot, KEGG, COG, and GO databases, respectively, and total annotation unigenes were 37,764. After 30 days of exposure to 55 μg Cu/l, a total of 292 and 1076 genes were significantly up- and down-regulated, respectively. By KEGG analysis, 660 had a specific pathway annotation. Subsequent bioinformatics analysis revealed that the differentially expressed genes were mainly related to lipid metabolism, immune system, apoptosis, and signal transduction, suggesting that these signaling pathways may be regulated by Cu exposure. The present study provides comprehensive sequence information for subsequent gene expression studies regarding S. hasta, and the transcriptome profiling after Cu exposure is also expected to improve our understanding of the molecular toxicology of Cu.