Abstract
Tibetan naked carp Gymnocypris przewalskii 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 G. przewalskii to extreme conditions in Lake Qinghai. We generate the first miRNAome of G. przewalskii in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in G. przewalskii, 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 G. przewalskii, 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 G. przewalskii to highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.
Highlights
MicroRNAs are a family of endogenous RNAs that regulated gene expression pattern at post-transcriptional level
The big progresses were made in unveiling mechanisms of speciation and environmental adaptation of G. przewalskii, especially the contributions from functional genes [10,12,13,16,17,18]
We found high miRNA sequence similarity between G. przewalskii and other 9 animal species analyzed here, and identified a number of conserved miRNAs
Summary
MicroRNAs (miRNAs) are a family of endogenous RNAs that regulated gene expression pattern at post-transcriptional level. Schizothoracinae fishes are the predominant fish fauna in the Tibetan Plateau (TP), which have more than 60 species widely distributed throughout TP altitudes [8,9]. These fish species have evolved specific genetic and phenotypic characteristics to adapt to extremely harsh aquatic environments, such as chronic cold, hypoxia, saline and alkaline aquatic environments [8,10,11]. Recent studies have identified key genes contributing to speciation and adaptation of G. przewalskii [12,16,19], but little is known on role of miRNAs in the adaptation of G. przewalskii to extreme aquatic environment in Lake Qinghai. We combine small RNA sequencing of G. przewalskii and multiple bioinformatics analyses to uncover function of miRNAs in high altitude adaptation
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