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Transcriptome profiling and digital gene expression analysis of Nile tilapia (Oreochromis niloticus) infected by Streptococcus agalactiae

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Abstract

Tilapia is an important freshwater aquaculture species worldwide. In recent years, streptococcal diseases have severely threatened development of tilapia aquaculture, while effective prevention and control methods have not yet been established. In order to understand the immunological response of tilapia to infection by Streptococcus agalactiae (S. agalactiae), this study employed Solexa/Illumina RNA-seq and digital gene expression (DGE) technology to investigate changes in the tilapia transcriptome before and after S. agalactiae infection. We obtained 82,799 unigenes (mean size: 618 bp) using de novo assembly. Unigenes were annotated by comparing against databases including Nr, Swissprot, cluster of orthologous groups of proteins, Kyoto encyclopedia of genes and genomes, and gene ontology. Combined with DGE technology, transcriptomic changes in tilapia before and after bacteria challenging were examined. A total of 774 significantly up-regulated and 625 significantly down-regulated unigenes were identified, among which 293 were mapped to 181 signaling pathways including 17 immune-related pathways involving 65 differentially expressed genes. We observed a change in the expression of six genes in the Toll-like receptor signaling pathway, and this was subsequently confirmed via quantitative real-time PCR. This comparative study of the tilapia transcriptome before and after S. agalactiae infection identified important differentially-expressed immune-related genes and signaling pathways that will provide useful insights for further analysis of the mechanisms of tilapia defense against S. agalactiae infection.

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Acknowledgments

This work was supported by grants from the National High-tech R&D Program of China (863 Program, No.2011AA100404), National Natural Science Foundation of China (N0.31272688) and China Agriculture Research System (CARS-49). We would like to thank Dr. Mark R. Liles at Auburn University, US for editorial help.

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Authors and Affiliations

  1. Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, China Ministry of Agriculture, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China

    Rui Zhang, Li-li Zhang, Xing Ye, Yuan-yuan Tian, Cheng-fei Sun, Mai-xin Lu & Jun-jie Bai

  2. College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China

    Rui Zhang

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  1. Rui Zhang
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  2. Li-li Zhang
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  3. Xing Ye
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Correspondence to Xing Ye.

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Zhang, R., Zhang, Ll., Ye, X. et al. Transcriptome profiling and digital gene expression analysis of Nile tilapia (Oreochromis niloticus) infected by Streptococcus agalactiae . Mol Biol Rep 40, 5657–5668 (2013). https://doi.org/10.1007/s11033-013-2667-3

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