Transcriptional response to low temperature in the yellow drum (Nibea albiflora) and identification of genes related to cold stress

The yellow drum (Nibea albiflora) is an economically important maricultured fish in China, but the aquaculture of this species is severely affected by overwinter mortality associated with cold stress. Characterization of the molecular mechanisms underlying the susceptibility of the yellow drum to cold might increase our understanding of how this fish adapts to environmental challenges. Here, the transcriptional response of the yellow drum to cold stress (7.5 degrees C) was investigated with RNA-Seq analysis. We compared brain and muscle transcriptomes among cold-tolerant (Tol) fish that survived the cold treatment, cold-sensitive (Sen) fish that were killed by the cold treatment, and control (Con) fish that were not subjected to cold. Our analysis recovered 233,245 unigenes. The genes (DEGs) differentially expressed in the brain and muscle of the Tol versus Con group, the Sen versus Con group, and the Tol versus Sen group had tissue-specific expression patterns. Gene ontology, enrichment, and pathway analyses indicated the most highly enriched pathways in the DEGs were signaling molecules and interaction, signal transduction, carbohydrate metabolism, lipid metabolism, digestive system, and endocrine system pathways. These pathways were all associated with biological functions relevant to cold adaptation in the yellow drum, including transduction of stress signals, energy metabolism, and stress induced cell membrane changes. We identified genes likely to be involved in cold-susceptibility and -tolerance as those differentially expressed in the Tol group as compared to the Sen group. Further investigation and characterization of these candidate genes might improve our understanding of the mechanisms underlying cold adaptation in the yellow drum.