Triplophysa scleroptera Raw sequence reads

Triplophysa fishes are the main component of fish fauna in the Qinghai-Tibet Plateau, which have well adapted to the high altitude environment. Despite their importance, the genetic mechanism of adaptation to Tibet remains poorly understood. With the advent of next-generation sequencing methods, however, it is now possible to reveal potential molecular mechanisms of highland adaptation. Here, we sequenced the transcriptomes of T. scleroptera and T. siluroides, and used them to identify potential genetic mechanisms of high altitude adaptation. An analysis of 2269 orthologous genes among Astyanax mexicanus, Danio rerio, Paramisgurnus dabryanus, T. scleroptera, T. siluroides, and T. dalaica revealed each terminal branch of the Triplophysa fishes has a significantly higher ratio of nonsynonymous to synonymous substitutions than other branches, providing evidence for genome-wide accelerated evolution in Triplophysa lineage. Many rapidly evolving GO categories in Triplophysa fishes relative to P. dabryanus were significantly enriched for these functions related to the hypoxia response and energy metabolism. Genes exhibiting signs of positive selection and fast evolution in the Triplophysa lineage also have functional roles involved in energy metabolism and high altitude hypoxia. The results from this study should have important implications for our understanding of the evolution of Triplophysa fishes and their adaptations to the Qinghai-Tibet Plateau.