Takifugu obscurus has relatively small gills and gill pores, leading to a relatively low respiratory capacity and increased vulnerability to low dissolved oxygen (DO) levels compared to other fish. To investigate the responses of T. obscurus to acute hypoxic stress, high-throughput-sequencing-based transcriptomic analyses were conducted here to assess the responses of T. obscurus gills to acute hypoxic stress. Three environmental conditions were compared including normoxia (DO: 7.0 ± 0.2 mg/L), hypoxic stress (DO: 0.9 ± 0.2 mg/L), and reoxygenation (4, 8, 12, and 24 h after return to normoxia) conditions to identify differentially expressed genes (DEGs) responsive to hypoxia. A total of 992, 877, 1561, 1412, and 679 DEGs were identified in the normoxia and reoxygenation for 4, 8, 12, and 24 h groups in comparison to the hypoxia groups, respectively. The DEGs were primarily associated with oxidative stress, growth and development, and immune responses. Further functional annotation enrichment analysis of the DEGs revealed that they were primarily related to cytokine–cytokine interactions, transforming growth factor β receptor (TGF-β), cell adhesion molecules (CAMs), the vascular endothelial growth factor (VEGF) signaling pathway, and the mitogen-activated protein kinase (MAPK) signaling pathway. These results provide new insights into the physiological and biochemical mechanisms of T. obscurus adaptations to hypoxic stress. Furthermore, these results provide a framework for future studies into the molecular mechanisms of hypoxia tolerance and the healthy culture of T. obscurus and other fish.

• TMT-based proteomics was used to study and compare the muscle protein profiles of Pacific abalones between northern and southern China. • 729 differential abundance proteins were identified in different regions. • Fatty acid synthase and other 3 proteins were identified as candidate biomarkers for identification of northern and southern abalone.