3.5 Multi-omics identification of key miRNAs, genes, proteins, and metabolites
The hierarchical clustering of the DEP, DEMI, DEG and DEM based on the fold change’ Z score of M4a/(M4b, M4c, M0a, M0b, M0c), six samples’ log10 (Norm), six samples’ Z score of TPM and 20 samples’ Z score of Norm were showed that all samples can be divided into two different groups according to control and hypoxia treatment (Fig. S1) . In general, environmental hypoxia had a significant effect on the overall gene /miRNA/ protein/metabolite expression profile of P. vachellimuscle.
In this study, the transcriptome, miRNAome, proteome and metabolome ofP. vachelli muscle under hypoxia stress were integrated by investigating whether changes in “genes/proteins” levels correlated with changes in the corresponding “negative miRNAs”, and coupled with mutual KEGG pathways for DEM. This was based on 145 negative miRNA-mRNA-protein pairs and 33 unique DEM, 16 DEMI, 23 co-DEG/DEP and 17 DEM were involved in the 19 mutual KEGG pathways (Fig. 4B ).
These mutual pathways contained carbohydrate metabolism (i.e., TCA cycle, pentose phosphate pathway, starch, sucrose, pyruvate, butanoate, glyoxylate and dicarboxylate metabolism), amino acid metabolism (i.e., valine, leucine, isoleucine, cysteine, methionine, alanine, aspartate, glutamate, D-Glutamine and D-glutamate metabolism), other metabolic processes (i.e., purine and nitrogen metabolism, biosynthesis of aminoacyl-tRNA, unsaturated fatty acids, butirosin and neomycin), membrane transport (i.e., ABC transporters), signal transduction (i.e., mTOR signaling pathway), and cellular community (i.e., gap junction). Genes produce proteins through complex transcription and translation processes to regulate the metabolism of organisms (Table S5 ). In our case, downregulated miR-193b/457a/15b-OGDH, miR-210/338-SDHb, and miR-457a/214-MDH1 led to suppression of aerobic metabolism (e.g., “Pyruvate metabolism” and “TCA cycle”), thus making intermediate products rise (e.g., citric acid and S-lactoylglutathione). “Aminoacyl-tRNA biosynthesis” was regulated by downregulated miR-15b/338/457a-Aars/mars and miR-133b/18a/PC-7236-hars to accumulate intermediates (proline, isoleucine, and methionine).