Supporting data for "Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation"

Intense stresses caused by high-altitude environments may result in noticeable genetic adaptions in native species. Studies of genetic adaptations to high elevations have been largely limited to terrestrial animals. How fish adapt to the high-elevation environments is largely unknown. <i>Triplophysa bleekeri</i>, an endemic fish inhabiting high-altitude regions, presents an excellent model to investigate the genetic mechanisms of adaptation to the local environment. Here, we assembled a chromosomal genome sequence of about 628 Mb with a contig and scaffold N50 of 3.1 and 22.9 Mb, respectively. We investigated the origin and environmental adaptation of <i>T. bleekeri</i> based on 21,198 protein-coding genes in the genome. Compared to fish species living at low altitudes, gene families associated with lipid metabolism and immune response were significantly expanded in the <i>T. bleekeri</i> genome. Genes involved in DNA repair exhibit positive selection for <i>T. bleekeri</i>, <i>T. siluroides</i>, and <i>T. tibetana</i>, indicating that adaptive convergence in <i>Triplophysa</i> species occurred at the positively selected genes. We also analyzed whole-genome variants among samples from three populations. The results showed that populations separated by geological and artificial barriers exhibited obvious differences in genetic structures, indicating that gene flow is restricted between populations. These results will help us expand our understanding of environmental adaptation and genetic diversity of <i>T. bleekeri</i>, and provide valuable genetic resources for future studies on the evolution and conservation of high-altitude fish species such as <i>T. bleekeri</i>