Integrated analysis of mRNA and miRNA expression profiles in Ptychobarbus dipogon and Schizothorax oconnori, insight into genetic mechanisms of high altitude adaptation in the schizothoracine fishes

The schizothoracine fishes with three evolutionary grades adapt well to various altitude environments, and show significant differences in adaptive characters. To understand the genetic mechanisms of high altitude adaptation, this study aims to compare the mRNA and miRNA expression profiles in Ptychobarbus dipogon and Schizothorax oconnori which represent the specialized and primitive schizothoracine fishes, respectively. For the mRNAs, a total of 10,513 up-regulated and 7212 down-regulated unigenes were identified in P. dipogon. For the miRNAs, a total of 225 and 229 conserved miRNAs were identified from P. dipogon and S. oconnori, respectively, and among them, 66 up-regulated and 40 down-regulated miRNAs were identified in P. dipogon. The top ten different fold change miRNAs were dre-miR-25, dre-miR-451, dre-miR-27b, dre-miR-222, dre-miR-153b, dre-miR-727*, dre-miR-732, dre-let-7g, dre-miR-203b* and dre-let-7f. Integrated analysis of mRNA and miRNA expression profiles predicted 2949 genes involved in the miRNA-mRNA interaction. Among them, up-regulated genes were significantly enriched in ribosome biogenesis in eukaryotes, tight junction and spliceosome pathways, and down-regulated genes were assigned to metabolic pathways, propanoate metabolism and fatty acid metabolism pathways. These results may demonstrated that P. dipogon adapt the higher altitude environment through deceleration of metabolism and enhancement of transcription.