Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Genomics. 2017 Dec 6;18(1):948. doi: 10.1186/s12864-017-4352-8.
Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined.
Our study used comparative genomic analysis based on the transcriptomic data of G. p. ganzihonensis and other four fish genome datasets to investigate the genetic basis of highland adaptation in Schizothoracine fish. We found that Schizothoracine fish lineage on the terminal branch had an elevated dN/dS ratio than its ancestral branch. A total of 202 gene ontology (GO) categories involved into transport, energy metabolism and immune response had accelerated evolutionary rates than zebrafish. Interestingly, we also identified 162 genes showing signature of positive selection (PSG) involved into energy metabolism, transport and immune response in G. p. ganzihonesis. While, we failed to find any PSG related to hypoxia response as previous studies.
Comparative genomic analysis based on G. p. ganzihonensis transcriptome data revealed significant genomic signature of accelerated evolution ongoing within Tibetan Schizothoracinae species lineage. Molecular evolution analysis suggested that genes involved in energy metabolism, transport and immune response functions in Schizothoracine fish underwent positive selection, especially in innate immunity including toll-like receptor signaling pathway genes. Taken together, our result as a case study in Schizothoracinae species provides novel insights in understanding the aquatic animal adaptation to extreme environment on the Tibetan Plateau, and also provides valuable genomic resource for further functional verification studies.
关于陆生动物高原适应机制的全基因组研究已有广泛报道，而水生动物的相关研究则较少。藏鲃属物种是研究鱼类物种形成和适应的理想模式系统。藏鲃属鱼类细鳞裂腹鱼曾经历从咸水到淡水的生态位转移，并且最近与青海湖裸鲤发生分化。此外，细鳞裂腹鱼栖息在包括低温和缺氧在内的恶劣水生环境中，与其他藏鲃属物种一样，其高原适应的遗传机制尚未确定。
本研究基于细鳞裂腹鱼的转录组数据和其他四个鱼类基因组数据集进行比较基因组分析，以研究藏鲃属鱼类高原适应的遗传基础。我们发现，藏鲃属鱼类末端支系的 dN/dS 比值高于其祖先支系。共有 202 个参与运输、能量代谢和免疫反应的基因本体 (GO) 类别具有比斑马鱼更快的进化速率。有趣的是，我们还鉴定出 162 个与能量代谢、运输和免疫反应相关的基因在细鳞裂腹鱼中表现出正选择 (PSG) 的特征。然而，我们没有发现任何与先前研究中缺氧反应相关的 PSG。
基于细鳞裂腹鱼转录组数据的比较基因组分析揭示了藏鲃属物种支系内正在进行的显著基因组加速进化特征。分子进化分析表明，参与能量代谢、运输和免疫反应功能的基因在藏鲃属鱼类中经历了正选择，特别是在先天免疫中，包括 Toll 样受体信号通路基因。综上所述，作为藏鲃属物种的案例研究，我们的结果为理解青藏高原极端环境下水生动物的适应提供了新的见解，并为进一步的功能验证研究提供了有价值的基因组资源。
