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Transcriptome characterization and gene expression of Epinephelus spp in endoplasmic reticulum stress-related pathway during betanodavirus infection in vitro

Ming-Wei Lu12*, Fang-Huar Ngou1, Yung-Mei Chao3, Yu-Shen Lai4, Nai-Yu Chen5, Fan-Yao Lee5 and Pinwen P Chiou5*

Author affiliations

1 Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan

2 Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan

3 Institute of Basic Medical Science, National Cheng Kung University, Tainan, Taiwan

4 Institute of Biotechnology, National Ilan University, Yilan, Taiwan

5 Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan

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Citation and License

BMC Genomics 2012, 13:651  doi:10.1186/1471-2164-13-651

Published: 21 November 2012



Grouper (Epinephelus spp) is an economically important fish species worldwide. However, viral pathogens such as nervous necrosis virus (NNV) have been causing severe infections in the fish, resulting in great loss in the grouper aquaculture industry. Yet, the understanding of the molecular mechanisms underlying the pathogenicity of NNV is still inadequate, mainly due to insufficient genomic information of the host.


De novo assembly of grouper transcriptome in the grouper kidney (GK) cells was conducted by using short read sequencing technology of Solexa/Illumina. A sum of 66,582 unigenes with mean length of 603 bp were obtained, and were annotated according to Gene Ontology (GO) and Clusters of Orthologous Groups (COG). In addition, the tag-based digital gene expression (DGE) system was used to investigate the gene expression and pathways associated with NNV infection in GK cells. The analysis revealed endoplasmic reticulum (ER) stress response was prominently affected in NNV-infected GK cells. A further analysis revealed an interaction between the NNV capsid protein and the ER chaperone immunoglobulin heavy-chain binding protein (BiP). Furthermore, exogenous expression of NNV capsid protein was able to induce XBP-1 mRNA splicing in vivo, suggesting a role of the capsid protein in the NNV-induced ER stress.


Our data presents valuable genetic information for Epinephelus spp., which will benefit future study in this non-model but economically important species. The DGE profile of ER stress response in NNV-infected cells provides information of many important components associated with the protein processing in ER. Specifically, we showed that the viral capsid protein might play an important role in the ER stress response.