1. Introduction
Aerobic animals use oxygen to generate energy through oxidative phosphorylation within mitochondria. Currently, aquatic ecosystems are increasingly under pressure from pollutants, nutrient enrichment, and global warming, all of which more increase the risk of hypoxia in water (Mandicet al. 2015). Therefore, aquatic organisms are usually exposed to different concentrations of dissolved oxygen.  A severe and sudden hypoxia can be fatal for hypoxia-sensitive fish. Revealing the molecular mechanism of fish hypoxia adaptation will help us find the hypoxic marker caused by environmental stress (Abdelrahman et al. 2017).
In order to maintain organism function and homeostasis in a hypoxic environment, aquatic organisms, including fishes, respond by various behavioral and physiological adjustments, e.g., decreasing swimming rate, increasing respiration rate, increasing oxygen supply, and reducing oxygen consumption (Sappalet al. 2016; Zhong et al.2009). These process depends on the division and cooperation among tissues in fishes, such as liver, muscle, brain, heart, gill. Relevant research results show that there are differences in the sensitivity and tolerance of different tissues, indicating that the tissue-specific expression pattern reflects the different metabolic effects of tissues during hypoxia (Zhu et al. 2013). For example, fish brain and heart showed fewer examples of down-regulation compared with muscle, in keeping with the need for sustained activity (Gracey et al. 2001; Lardon et al. 2013). The different patterns may also be related to the extent of the hypoxic insult that each tissue experiences. For example, fish heart receives blood directly from the gills and thus will have a better oxygen supply than other tissues (Everett et al. 2012; Ju et al. 2007).
Now, various methods in fish were applied for studies of the hypoxia molecular mechanisms, e.g., investigations for transcriptional changes using qRT-PCR (Chen et al. 2012; Wang et al. 2015), transcriptome (Beck et al. 2016; Gong et al. 2020; Yang et al. 2018), and changes in protein using 2D-DIGE (Dowd et al.2010; Smith et al. 2009; Wulff et al. 2012). Biological phenomena induced by environmental stress are changeable and complex, which is also accompanied by complicated regulation of miRNA/gene/protein expression. Multiple omics are combination of two or more omics methods, and can avoid the incomprehensive conclusions of single-omics (Sun et al. 2018). Unfortunately, the study of the fishes responding mechanism undergo hypoxia using multi-omics is negligible, which vastly hinders the comprehensive understanding of this biological phenomenon.
Pelteobagrus vachelli has become a popular commercial fishes in Asia because of its relatively high yield and an affordable price for consumers (Guosong et al. 2017). However, due to its low oxygen threshold and high oxygen consumption rate, this species is only found in the rivers. A sudden lack of oxygen can result in mortality and finally cause the pond turnover (Zhang et al. 2016a). These properties indicate that P. vachelli is not only an important aquaculture variety, but also a potential model fishes for studying the molecular mechanisms of hypoxia. Recently, the miRNA-mRNA regulatory network has been shown to respond to hypoxia in livers ofMegalobrama amblycephala (Sun et al. 2017) and P. vachelli (Zhanget al. 2016b). This suggests that the HIF-1 signaling may be involved in fish hypoxic molecular adaptation, which is often regulated and controlled by the physiological changes. Also, we conducted iTRAQ proteomic analysis in P. vachelli livers to uncover hypoxic responsive proteins involved in diverse biological pathways, e.g., peroxisome, glycolysis, PPAR signaling, lipid and amino acid metabolism (Zhang et al. 2017).
At present, relative to other tissues, studies on the mechanism of fish muscle, the largest tissue, response to hypoxia are relatively scarce. Therefore, we characterize transcriptomic, miRNAomic, proteomic and metabolomic changes of P. vachellimuscles under environmental hypoxia simultaneously (Fig. 1 ), combined with the previous studies on P. vachelli liver. Our findings aim to offer deeper insights into tissue-specific patterns of expression induced by environmental hypoxia, on the other hand the methods and study design can be used to analyze markers to profile other species undergo hypoxic environmental stress.