Currently, no genome is available for Tibetan fish species, Schizothoracinae (Cyprinidae) is the main fish species and widely distributed on the Tibetan Plateau (TP). The evolution of morphology and population diversity in Schizothoracinae coupled with the uplift of TP. This dearth of Schizothoracinae genomic resources greatly restricts genomic studies of Tibetan fish and, more generally, our understanding of teleost fish genome evolution. To fill this gap, we provide the de novo transcriptome of 8 tissues from a Tibetan fish, Gymnocypris przewalskii, and compare it to that of zebrafish, common carp and other teleost fish. Approximately 1.2 billion clean reads (8 datasets mixed) from the G. przewalskii were generated. All clean reads were assembled into 268,872 unigenes and annotated by public databases. Phylogeny analysis based on large number of single copy genes suggests that G. przewalskii having diverged approximately 29.95 Mya with common carp and 52.15 Mya with zebrafish. Comparative genome analysis revealed that 241 species-specific genes are in G. przewalskii and most related to metabolism, implied that this type of gene had underwent large-scale duplication. Our analysis also identifies 164 fast evolving genes and 76 positive selection genes (PSG), most of genes related to metabolism and immunity. Interestingly, we identified 23 PSGs involved into epigenetics changes, including DNA methyltransferase, N-acetyltransferase, indicated these genes may undergo neofunctionalization or sub functionalization under strong positive selection. The reference transcriptome of G. przewalskii offers an improved understanding of evolution of teleost fish genomes and also provides novel insights on fish adaptation to high altitude.
