The microRNA repertoire of Tibetan naked carp <i>Gymnocypris przewalskii</i>: A case study in Schizothoracinae fish on the Tibetan Plateau

<div><p>Tibetan naked carp <i>Gymnocypris przewalskii</i> is an ideal model system to study highland adaptation of fish, because it evolved specific genetic and phenotypic characteristics to adapt to chronic cold and alkaline environments in Lake Qinghai. MicroRNAs (miRNAs) are small noncoding RNAs that regulating gene expression post-transcriptionally in a wide range of biological processes. In this study, we focus on the role of miRNAs in adaptation of <i>G</i>. <i>przewalskii</i> to extreme conditions in Lake Qinghai. We generate the first miRNAome of <i>G</i>. <i>przewalskii</i> in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in <i>G</i>. <i>przewalskii</i>, and also identified 15 teleost-specific miRNAs. Using a large scale of conserved miRNAs, we constructed a high-confidence phylogenetic tree between teleost and mammals than mitochondria and nuclear genes. In addition, we found that several miRNA family (e.g. miR-10 and let-7) members highly expressed in <i>G</i>. <i>przewalskii</i>, which may function in multiple biological processes. Finally, we predicted a total of 34,258 miRNA targets genes. Conserved miRNAs target genes participating in signal transduction, cell differentiation and biosynthetic process, and showed signature of functional constraint. While novel miRNAs in a species displayed species-specific targets and involved in ion binding, transport and oxidoreductase activity, may affect the expression patterns of targets with signature of gene family expansion or positive selection under extreme environment. Taken together, this study demonstrated that miRNAs may involve into roles of adaptation of <i>G</i>. <i>przewalskii</i> to highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.</p>