裂腹鱼类基因组多倍化及其对青藏高原极端环境的适应机制研究

Whole genome duplication, or polyploidy, provides a shortcut to add the genetic material for adaptive evolution, and is the major driving force behind speciation and diversification. However, the question that the evolutionary dynamics of polyploidy in schizothoracine fishes and its implication for adaptation to the extreme environment of the Tibetan Plateau, has not been determined. In this project, we will perform deep transcriptome sequencing for the schizothoracine fishes endemic to the Tibetan Plateau. Using the methods of bioinformatics, comparative genomics, and molecular evolution, we attempt to analyze the times and ages of whole genome duplication, and the relationship to the process of uplift of the Tibetan Plateau. We will also determine the patterns of paralog retention, divergence on the DNA and RNA level, and their roles to adaptation to the extreme environment of the Tibetan Plateau. Furthermore, we will compare the molecular characteristics between schizothoracine fishes and the fishes in low altitude, including evolutionary rates, genes under positive selection, and lineage specific genes. And we will test our results by experimental analysis. The object of the project is to understand the genetic mechanisms of adaptation to the extreme environment of the Tibetan Plateau in schizothoracine fishes at the genomic level.

全基因组复制（多倍化）为生物适应性进化提供了快速增加遗传物质的捷径，是物种形成与分化的重要驱动力。然而，对于“多倍化在裂腹鱼类中的进化历程及其与适应青藏高原极端环境的关系”这一科学问题还未曾研究。本项目将以青藏高原特有的三个不同进化等级的裂腹鱼类为研究对象，采用高深度转录组测序技术，运用生物信息学、比较基因组学及分子进化等分析方法，重点研究裂腹鱼类进化过程中发生的多倍化事件次数、发生时间及其与青藏高原三次剧烈隆升之间的联系。同时探讨多倍化产生的重复基因的保留过程，在序列水平（DNA）和表达水平（RNA）上的分化情况与高原极端环境适应性的关系。此外，深入对比裂腹鱼类与低海拔鱼类的分子特征，包括进化速率、正选择基因及谱系特异新基因等，并对重要功能基因进行实验验证，以期从全基因组水平阐述裂腹鱼类适应青藏高原极端环境的遗传学机制。

本研究项目对分布于青藏高原及其邻近地区56种裂腹鱼进行了转录组测序，组装，系统发育分析，分歧时间估算，进化速率分析，正选择及快速进化基因检测。主要结果有：1.裂腹鱼亚科鱼类不是单系群。其中，原始等级裂腹鱼类是单系群，特化等级裂腹鱼类和高度特化等级裂腹鱼类不是单系群。原始等级裂腹鱼类与鲈鲤构成姐妹群关系，少鳞舟齿鱼是裂腹鱼类的姐妹群；2.裂腹鱼类是按照水系分布聚类在一起，邻近水系的物种亲缘关系更近；3.裂腹鱼类的起源时间约为2600万年前，与青藏高原的隆升过程相吻合；4.裂腹鱼类相对于非裂腹鱼类，其进化速率显著加快；5.裂腹鱼类中的正选择基因及快速进化基因均显著富集于低氧、能量代谢的功能中。