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Simple Summary: Silver sillago (Sillago sihama) is a marine fish species with a high economic value. S. sihama is poorly resistant to hypoxia. However, hypoxia stress-related genes and pathways in S. sihama remain unclear. In this study, we compared gill tissues of S. sihama between hypoxia and normoxia groups and detected differentially expressed genes under hypoxia stress. Two gene families, such as cytochrome P450 and glutathione S-transferase were associated with the function of metabolic process under the hypoxia stress. This study will expand our knowledge about the molecular mechanism of the transcriptome response to hypoxia stress in S. sihama.Abstract: Silver sillago (Sillago sihama) is a commercially important marine fish species in East Asia. In this study, we compared the transcriptome response to hypoxia stress in the gill tissue of S. sihama. The fish were divided into four groups, such as 1 h of hypoxia (hypoxia1h, DO = 1.5 ± 0.1 mg/L), 4 h of hypoxia (hypoxia4h, DO = 1.5 ± 0.1 mg/L), 4 h of reoxygen (reoxygen4h, DO = 8.0 ± 0.2 mg/L) after 4 h of hypoxia (DO = 1.5 mg/L), and normoxia or control (DO = 8.0 ± 0.2 mg/L) groups. Compared to the normoxia group, a total of 3550 genes were identified as differentially expressed genes (DEGs) (log 2 foldchange > 1 and padj < 0.05), including 1103, 1451 and 996 genes in hypoxia1h, hypoxia4h and reoxygen4h groups, respectively. Only 247 DEGs were differentially co-expressed in all treatment groups. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, DEGs were significantly enriched in steroid biosynthesis, biosynthesis of amino acids, glutathione metabolism and metabolism of xenobiotics by cytochrome P450, ferroptosis and drug metabolism-cytochrome P450 pathways. Of these, the cytochrome P450 (CYP) and glutathione S-transferase (GST) gene families were widely expressed. Our study represents the insights into the underlying molecular mechanisms of hypoxia stress.Animals 2020, 10, 628 2 of 13 the aquatic environment, which can be accelerated by several factors, such as human activities, water pollution, and intensive fish farming [1]. To adapt to the hypoxic environment, fish produce a range of adaptive physiological mechanisms, such as a rapid change in cell metabolism using ATP [2], regulation of respiratory function [3], floating head [4], and neurological, immune, and hormonal responses [5]. Severe hypoxia can even affect fish reproduction, survival, and cell metabolism [6]. The fish gill is the primary organ for physiological exchanges with the surrounding environment [7]. The fish gill plays a dominant role in aquatic gas exchange and is capable of extensive remodeling in response to changes in the DO level [8]. Many fish respond to hypoxia by increasing the functional surface area of their gill [4]. When the fish returns to normoxic water, the hypoxia-induced gill remodeling is reversed due to the embedding of gill lamellae [9].The sillago silver (Sillago sihama) is a popular species of the family Sillaginidae [10]. S. sihama is ...