Triplophysa scleroptera Raw sequence reads. Triplophysa scleroptera

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.

高原鳅属（Triplophysa）鱼类是青藏高原鱼类区系的核心组成部分，已高度适应高海拔环境。尽管该类群具有重要的生态与科研价值，但学界对其适应青藏高原的遗传机制仍知之甚少。随着下一代测序技术的发展，如今我们得以揭示高原适应的潜在分子机制。本研究对硬刺高原鳅（Triplophysa scleroptera）与鲇高原鳅（Triplophysa siluroides）的转录组进行测序，并以此为基础解析高原适应的潜在遗传机制。通过对墨西哥丽脂鲤（Astyanax mexicanus）、斑马鱼（Danio rerio）、大鳞副泥鳅（Paramisgurnus dabryanus）、硬刺高原鳅、鲇高原鳅以及达来高原鳅（Triplophysa dalaica）共2269个直系同源基因的分析，研究发现高原鳅属鱼类的各末端分支的非同义替换与同义替换比值均显著高于其他分支，这为高原鳅属支系的全基因组进化加速现象提供了直接证据。相较于大鳞副泥鳅，高原鳅属鱼类中众多快速进化的基因本体（Gene Ontology, GO）功能类别显著富集于低氧应答与能量代谢相关通路。在高原鳅属支系中呈现正选择与快速进化特征的基因，同样参与能量代谢与高原低氧适应相关的生物学过程。本研究的结果将为我们理解高原鳅属鱼类的进化历程及其对青藏高原的适应机制提供重要的理论参考。