Transcriptional regulation and alternative splicing reveal the molecular strategies of Bombay duck Harpadon nehereus to hypoxia

Bombay duck Harpodon nehereus has undergone a dramatic shift from a by-catch fish species to the dominant species in the southeast coast of China. This shift has led to economic growth in the fishery and has had a significant impact on community structure, biodiversity, and resource competition in the ecosystem. Strong hypoxia tolerance may be one of the contributing factors for its population growth. This study compared the transcriptional regulation and alternative splicing in H. nehereus from the normoxic and hypoxic zone near the Yangtze Estuary. Compared with normoxia, the number of alternative splicing events increased in the gill and heart but decreased in the muscle after hypoxia, among which exon skipping was the most prevalent type in different tissues. Enrichment analysis showed that differentially expressed genes and genes with differentially alternative exons were mainly enriched in transmembrane transport and glycerophospholipid metabolic process in gill, cell cycle, and FoxO signaling pathway in heart, as well as cell cycle and reduced metabolic rate in muscle. Key candidate genes may be associated with gill remodeling, elevated heart rate, and muscle angiogenesis function. This study provides valuable genetic clues for evaluating molecular regulation strategies related to hypoxia tolerance in marine fishes.