Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.
University of Chinese Academy of Sciences, Beijing, China.
DNA Res. 2022 Jun 25;29(4). doi: 10.1093/dnares/dsac025.
Gymnocypris przewalskii, a cyprinid fish endemic to the Qinghai-Tibetan Plateau, has evolved unique morphological, physiological and genetic characteristics to adapt to the highland environment. Herein, we assembled a high-quality G. przewalskii tetraploid genome with a size of 2.03 Gb and scaffold N50 of 44.93 Mb, which was anchored onto 46 chromosomes. The comparative analysis suggested that gene families related to highland adaptation were significantly expanded in G. przewalskii. According to the G. przewalskii genome, we evaluated the phylogenetic relationship of 13 schizothoracine fishes, and inferred that the demographic history of G. przewalskii was strongly associated with geographic and eco-environmental alterations. We noticed that G. przewalskii experienced whole-genome duplication, and genes preserved post duplication were functionally associated with adaptation to high salinity and alkalinity. In conclusion, a chromosome-scale G. przewalskii genome provides an important genomic resource for teleost fish, and will particularly promote our understanding of the molecular evolution and speciation of fish in the highland environment.
青海湖裸鲤，一种特产于青藏高原的鲤科鱼类，已经进化出独特的形态、生理和遗传特征，以适应高原环境。在此，我们组装了一个高质量的青海湖裸鲤四倍体基因组，大小为 2.03Gb，支架 N50 为 44.93Mb，锚定在 46 条染色体上。比较分析表明，与高原适应相关的基因家族在青海湖裸鲤中显著扩张。根据青海湖裸鲤基因组，我们评估了 13 种高原鳅鱼类的系统发育关系，并推断青海湖裸鲤的种群历史与地理和生态环境的变化密切相关。我们注意到青海湖裸鲤经历了全基因组复制，并且复制后保留的基因与适应高盐度和高碱性有关。总之，一个染色体水平的青海湖裸鲤基因组为硬骨鱼类提供了一个重要的基因组资源，特别有助于我们理解鱼类在高原环境下的分子进化和物种形成。
