背景:关于陆生动物高原适应机制的全基因组研究已被广泛报道,但对水生动物的研究很少。西藏裂刺科物种是研究鱼类物种和适应性的理想模型系统。裂刺鱼,ganzihonensis经历了从盐水到淡水的生态位转变,并且最近也经历了与Gymnocyprisprzewalskiiprzewalskii的分裂。此外,G.p.ganzihonensis居住在恶劣的水生环境中,包括低温和缺氧以及其他裂刺科物种,其高原适应性的遗传机制尚未确定。
结果:我们的研究使用基于G.p.甘子鱼和其他四个鱼类基因组数据集的转录组数据进行比较基因组分析,以研究裂殖鱼鱼高原适应的遗传基础。我们发现,末端分支上的裂殖鱼系的dN/dS比率高于其祖先分支。共有202个基因本体论(GO)类别参与转运,能量代谢和免疫反应比斑马鱼进化速度加快。有趣的是,我们还鉴定了162个基因,显示出参与能量代谢的正选择(PSG)的特征,G.p.ganzihonesis的运输和免疫反应。同时,我们未能像以前的研究那样发现与缺氧反应相关的PSG.
结论:基于G.p.甘子菌转录组数据的比较基因组分析揭示了在西藏裂殖菌物种谱系中正在进行的加速进化的显著基因组特征。分子进化分析表明,参与能量代谢的基因,分裂胸科鱼类的运输和免疫反应功能经历了积极的选择,特别是在先天免疫中,包括toll样受体信号通路基因。一起来看,我们的结果作为一个案例研究,在了解水生动物对青藏高原极端环境的适应方面提供了新的见解,并为进一步的功能验证研究提供有价值的基因组资源。
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.