Liver transcriptome analysis and de novo annotation of the orange-spotted groupers (Epinephelus coioides) under cold stress.

Cold stress has caused great economic loss in fish culture worldwide. Orange-spotted grouper (Epinephelus coioides) is one of the most serious lost aquatic animals in 2016 cold fronts in South China. However, the molecular mechanism of grouper's cold resistance has remained largely unknown. In the present study, HiSeq™2000 (Illumina) was used to analyze the transcriptomic profiles of the liver from grouper under control temperature (CT, 28 °C) and low temperature (LT, 13 °C). Two normalized liver cDNA libraries of CT and LT groups were created. We obtained 51,944,970 and 51,905,036 clean reads from CT and LT groups, respectively. Comparing the LT group to the CT group, a total of 5905 significantly differentially expressed genes (DEGs) were identified, including 2093 up-regulated unigenes and 3812 down-regulated unigenes. GO annotation and functional enrichment analysis indicated that all of the DEGs were classified into three categories: biological process (23 subclasses), cellular component (18 subclasses) and molecular function (13 subclasses). KEGG analysis of the DEGs showed that 2732 DEGs were annotated to 253 signaling pathways. The most highly enriched pathways were cell adhesion molecules, Staphylococcus aureus infection, PPAR signaling pathway, Vibrio cholerae infection, primary immunodeficiency, fatty acid elongation, and we found cold stress mainly affects immunity, metabolic and signal transduction. Thirteen of the DEGs were further validated by qRT-PCR. Our results provide valuable information for further analysis of the mechanisms of groupers response under cold stress.