基于离散SNP位点解析青海湖裸鲤(Gymnocypris przewalskii)对水温和盐度的适应性

Adaptability Analysis of Gymnocypris przewalskii to Water Temperature and Salinity Based on Outlier SNP Sites

青海湖裸鲤(Gymnocypris przewalskii)在长期的进化过程中逐渐适应了青海湖特殊的高原地理环境。为揭示青海湖裸鲤的适应性进化机制,采用基因分型测序(genotyping by sequencing, GBS)技术对6个群体72尾青海湖裸鲤开展离散单核苷酸多态性(single nucleotide polymorphism, SNP)位点筛选,探讨其可能受到自然选择作用的相关SNP位点,并对离散SNP位点所在contigs进行序列比对及功能注释。研究共得到1 566个高度变异的适应性离散SNP位点。NR(non-redundant protein sequences)注释显示,相似比例序列所占比例最高的前两个物种分别是鱇浪白鱼(Anabarilius grahami)和鲤(Cyprinus carpio)。GO注释分析发现,注释到细胞过程、代谢过程和结合的contigs较多。KEGG注释分析显示,注释到代谢通路和神经活性配体-受体相互作用通路的contigs最多,其中,注释到代谢通路的基因包括ctu1、cps1、gba2、fasn和plcg1等,推测这些基因与青海湖裸鲤的本地适应性相关。研究结果证明青海湖裸鲤可能形成了与温度、盐度等环境因子相关的本地适应性机制,研究结果为进一步深入探讨青海湖裸鲤的本地适应性机制提供了技术方法和数据支撑。

The naked carp(Gymnocypris przewalskii) has gradually adapted to the special plateau geography of Qinghai Lake during the long-term evolutionary process. In order to reveal the adaptive evolutionary mechanism of G. przewalskii, GBS(genotyping by sequencing) was used to screen 72 naked carp from 6 populations for outlier SNP(single nucleotide polymorphism) markers to explore the possible effects of natural selection on them, to explore the related SNP sites that may be affected by Natural selection, and to conduct Sequence alignment and functional annotation on the contigs where the discrete SNP contigs sites are located. A total of 1 566 highly variable adaptive outlier SNP sites were identified in the study. NR(non-redundant protein sequences) annotation showed that the top two species with the highest proportion of similar sequences were Anabarilius graham and Cyprinus carpio, respectively. GO annotation analysis revealed that more contigs were annotated to cellular process, metabolic process and binding. KEGG annotation analysis showed that the most contigs were annotated to metabolic pathways and neuroactive ligand-receptor interaction pathways. Among them, genes annotated to metabolic pathways included ctu1, cps1, gba2, fasn, plcg1, etc., which may be associated with the local adaptation of Gymnocypris przewalskii. The results demonstrate that G. przewalskii may have developed local adaptations related to environmental factors such as temperature and salinity, and provide technical methods and data to further explore the local adaptation mechanisms of G. przewalskii.