3.1 Transcriptome summary
A total of 28,696 unique genes had been identified from six cDNA libraries (M0a, M0b, M0c, M4a, M4b, and M4c) representing P. vachelli muscles (Table S2 ). The quality control analysis of the transcriptome is shown in Table S3, including sequencing quality control overview, trinity assembly results overview, gene/transcript length overview, and gene function checklist. We found that 3511 genes were significantly upregulated, whereas 1033 genes were significantly downregulated in response to hypoxia (P < 0.05 and Fold change > 2). By performing the KEGG pathway analyses for 4544 differentially expressed genes (DEG), a total of 22 pathways were identified that showed significant changes after hypoxia (P < 0.05) (Fig. 2A ).
Among these pathways (Fig. 2A ), the “VEGF signaling pathway” involved in mediating vasopermeability, angiogenesis, and vascular tone was first enriched. However, DEG of “African trypanosomiasis” reflected the biological process of anemia (hemoglobin synthesis, down-regulated). Afterwards catabolism and anabolism were the two most represented subclasses. In addition, some important subclasses have also been significantly enriched, including human immune and inflammation. Finally, we found that “DCM” and “HCM” represented the impaired muscle function, which were also significantly enriched (P< 0.05). Interestingly, the numbers of upregulated genes were generally greater than that of downregulation for biological process of vessel, catabolism, immune, inflammation, muscle dysfunction, and vice versa for anemia and anabolism.