At last the three paths of apoptosis (extrinsic, mitochondrial, and endoplasmic reticulum stress) were enriched by abundant DEG/DEP (Fig. 6 ). For instance in 145 negative miRNA-mRNA-protein pairs, Hadha was downregulated and promoted cell apoptosis by decreasing the acylation of monolysocardiolipin into cardiolipin via raised miR-1-2 (Taylor et al. 2012). And that GRP78 is expressed in large quantities under low oxygen to maintain the stability of the endoplasmic reticulum and protect cells (Reddyet al. 2003). Upregulation of miR-457a led to endoplasmic reticulum stress and hypoxia-induced apoptosis by targeting GRP78 inP. vachelli muscles (Table 1 and Fig. 5 ).
(3) Muscle dysfunction
Several of the KEGG enriched by multi-omics (P < 0.05) were associated with impaired contraction or dilation of heart muscle (DCM and HCM) and dyskinesia (Parkinson’s and Huntington’s disease), which suggested that hypoxia induces muscle dysfunction (Fig. 2 and Fig. 3A ). In addition, “Vascular smooth muscle contraction” and “Calcium signaling pathway” contained abnormal muscular and calcium overload related proteins that were significantly enriched by down DEP. For example, Atp2a1, a key regulator of muscle performance, contributed to calcium sequestration involved in muscular excitation/contraction (Odermattet al. 2000). Krt8 helps to link the contractile apparatus to dystrophin at the costamere of striated muscle (Ursitti et al. 2004). In our results (Table 1 and Fig. 5 ), let-7b was upregulated, whereas its target genes/proteins Atp2a1 and Krt8 were significantly downregulated. This supported the idea that calcium overload and muscle dysfunction were linked in hypoxia adaptation in P. vachelli .
To date, understanding of small RNAs in fishes is limited and informations regarding hypoxic miRNA markers are especially rare. Compared with other animals or cell models, 24 miRNAs reported previously as hypoxia-responsive were identified (e.g., miR-15b, 133b, 143, 146b, 181a, 193b, 27b, 301b, 338, 152, 18a, 30a/d, 126, 199a, 210, 214, 29b, 25, let-7b) from 39 DEMI in our results. These are thought to exert broad pleiotropic effects by targeting genes involved in cell cycle arrest, metabolism, apoptosis, cell survival and mitochondrial function (Bandara et al. 2017; Guimbellot et al. 2009; McCormick et al. 2010; Pocock 2011). Additionally, in fishes, the tendencies of miR-210, -193b, -181a expression among muscle were the same as the liver of P. vachelli(Zhang et al. 2016b) or M. amblycephala (Sun et al. 2017) . For example, in negative miRNA-mRNA-protein pairs (Table S4 ), several key enzymes of “TCA cycle”, e.g., miR-193b-OGDH and miR-210-SDHb/SUCLA2, were detected in our conjoint analysis. Moreover, the same result as Danio rerio that raised let-7b acts downstream of HIF-1α to repress cell proliferation through blocking cell cycle progression (Huang et al. 2017). Interestingly, several miRNA expressions in P. vachelli muscle were the opposite to that of liver (e.g., miR-27b, -143, -338), which may be due to different tissues or a metabolic disorder in muscle induced by hypoxia. For instance, data analysis of predicted multi-omics pairsin silico (Table S4 ), suggested that the possible mechanism that GAPVD1, a protein required for efficient endocytosis (Guillen et al. 2020), promoted catabolism in muscles under hypoxia by downregulating miR-27b/143. Furthermore, upregulating miR-338 negatively targeted key enzymes of glycolysis (HK1) and “oxidative phosphorylation” (SDH, Atp5a1, NDUFV1/S1) under hypoxic conditions in P. vachelli muscle (Aschrafi et al. 2012).