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De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure

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Abstract

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.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grants Nos. 31372547, 31422056, 31072226, and 30800850) and the Fundamental Research Funds for the Central Universities (Grant Nos. 2662015PY017, 2013PY073). We thank Beijing Genomics Institute (Shenzhen, China, http://english.big.cas.cn/) for cDNA library construction and Illumina sequencing.

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  1. Zhi Luo

    Present address: Department of Animal Sciences, Cornell University, Morrison Hall, Ithaca, NY, 14850, USA

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  1. Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of China, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China

    Qi-Liang Chen, Zhi Luo, Chao Huang, Ya-Xiong Pan & Kun Wu

  2. Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan, 430070, China

    Qi-Liang Chen, Zhi Luo, Chao Huang, Ya-Xiong Pan & Kun Wu

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  1. Qi-Liang Chen
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Chen, QL., Luo, Z., Huang, C. et al. De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure. Fish Physiol Biochem 42, 979–994 (2016). https://doi.org/10.1007/s10695-015-0190-2

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