International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 51 3.2 Changes in gene families related to energy metabolism Another genomic basis for catfish hypoxia tolerance is reflected in the modification and expansion of energy metabolism-related genes. First, many fish enhance their functions by amplifying copies of certain key metabolic protein genes under long-term hypoxic stress. For example, the oxygen-carrying protein myoglobin gene in the genome of walking catfish (Clarias batrachus) has been massively amplified, with 15 copies identified, while most non-gill fish have only 1-2 copies. Enzyme genes related to catfish hypoxia metabolic pathways also show adaptive changes. During acute hypoxia, the expression of glycolysis-related enzymes such as phosphofructokinase (PFK) and pyruvate kinase (PK) in catfish is upregulated, while the expression of fructose bisphosphatase (FBP), which is in the opposite direction of gluconeogenesis, is downregulated, which promotes the anaerobic decomposition of sugars to quickly supply energy (Ma et al., 2023; Xiao et al., 2024). Some genes related to mitochondrial function and oxidative phosphorylation have also undergone functional changes in hypoxia-tolerant fish. For example, studies have reported that freshwater fish inhibit mitochondrial respiratory chain activity to reduce ROS generation during hypoxia and reoxygenation. Catfish may reduce oxygen consumption and reduce oxidative damage in hypoxia by regulating the expression of mitochondrial respiratory enzyme genes. 3.3 Antioxidant and stress response genes During the process of oxygen supply reduction and recovery, a large amount of reactive oxygen species (ROS) will be generated, causing oxidative damage to cells. Therefore, hypoxia-tolerant fish have evolved a strong antioxidant defense system. Under hypoxic stress, catfish activate a variety of antioxidant enzymes and molecular chaperone genes to reduce oxidative stress. Catfish minimizes oxidative damage caused by hypoxia by regulating antioxidant-related gene networks (including improving ROS clearance, initiating chaperone protection, and inhibiting inflammation). This efficient molecular stress response ability is also an important guarantee for its hypoxia-tolerant survival, which is highly consistent with the antioxidant adaptation observed in other hypoxia-tolerant fish (such as crucian carp, loach, etc.) (Abdel-Tawwab et al., 2019). Studies on Indian catfish have shown that hypoxia can upregulate the expression of genes such as HSP90 and HSP70, which helps stabilize the intracellular protein structure and prevent denaturation and aggregation (Mohindra et al., 2015). In addition, catfish often activate stress signaling pathways such as NF-κB when hypoxic, triggering cellular defense and repair mechanisms (Xing et al., 2025). 3.4 Evolution of the hemoglobin gene family As an oxygen transport carrier, the evolution of the hemoglobin gene family has a profound impact on the hypoxia tolerance of fish. Hemoglobin in teleost fish is usually encoded by multiple pairs of α and β subunit genes, which originated from the fish genome duplication event and underwent functional differentiation. Li et al. (2018) reported that the mRNA level of hemoglobin genes in the suprapharyngeal organs (auxiliary respiratory organs) of walking catfish was much higher than that in the gills, reflecting that the fish increased the efficiency of oxygen uptake from the air by highly expressing hemoglobin in the air breathing organs. On the other hand, the affinity and synergistic effect of hemoglobin for oxygen in different fish species vary, which is related to the amino acid sequence variation of hemoglobin genes. Hypoxia-tolerant fish often evolve hemoglobin with higher oxygen affinity so that they can more efficiently take up oxygen from water in hypoxic water environments. For example, hemoglobin mutations in many plateau fish increase oxygen affinity, thereby enhancing survival in hypoxic high-altitude environments (Borowiec et al., 2020). Although the research on the oxygen-binding properties of catfish hemoglobin is relatively limited, it is speculated that catfish may have moderate hemoglobin oxygen affinity and the ability to regulate pH by the Bohr effect so that it can maintain oxygen transport function under stress such as hypoxia and acidosis. 4 Catfish Population Genome and Adaptive Evolution to Hypoxia 4.1 Genome comparison and selection signal analysis Evidence from population genome and comparative genomics shows that the formation of catfish hypoxia tolerance involves the adaptive evolution of multiple key genes. This includes the variation and selection of
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