鲟鱼基因组加倍过程中的基因复制与进化

Gene replication and evolution in genome duplication of sturgeons

  • 摘要: 【目的】探究7种鲟鱼的系统发育关系及全基因组复制(WGD)事件,明确八倍体鲟鱼中高度复制基因特点和血红蛋白基因家族扩张时间,为揭示鲟形目鱼类基因组加倍事件及其进化策略提供理论依据。【方法】采集3种四倍体鲟鱼(闪光鲟、小体鲟和欧鳇)及4种八倍体鲟鱼(俄罗斯鲟、施氏鲟、达氏鳇和中华鲟)的血液样本,经Illumina测序后构建基因组草图,通过基因家族分析及重构系统发育树分析基因家族膨胀和收缩事件,基于同义替换率(Ks)和四倍简并位点颠换率(4DTv)估算WGD事件发生时间,通过血红蛋白基因家族进化分析推测基因家族分歧时间,比较八倍体和四倍体鲟鱼基因区域覆盖深度差异筛选出在八倍化事件中得到扩增且保留的高复制基因,并进行KEGG信号通路富集分析及蛋白互作网络(PPI)分析。【结果】7种鲟鱼基因组中存在大量的多拷贝直系同源基因,但共有单拷贝直系同源基因数量极少(仅26个);不同倍性鲟鱼间存在明显的基因家族膨胀和收缩事件,且四倍体鲟鱼与八倍体鲟鱼的基因保留模式不同。综合4DTv分析和Ks计算结果可知,所有鲟鱼均经历了1次古老的鲟形目特异性WGD事件(As3R),其发生时间在1.18亿~1.96亿年前,接近二叠纪—三叠纪大灭绝事件时期。八倍体鲟鱼的血红蛋白基因拷贝数分化明显,α血红蛋白基因拷贝数比为达氏鳇∶俄罗斯鲟∶施氏鲟∶中华鲟=3∶5∶4∶8,β血红蛋白基因拷贝数比为达氏鳇∶俄罗斯鲟∶施氏鲟∶中华鲟=4∶20∶4∶8。219个在八倍体鲟鱼中显著扩增且保留的高复制基因主要富集在基础代谢过程及与基因稳定性和表达调控密切相关的通路上,而蛋白互作网络图显示核心基因(PPFIA2ZAP70IRG1)在神经系统发育及免疫调节中发挥关键作用。【结论】WGD事件导致剪接体复合物、DNA修复等信号通路的相关基因在八倍体鲟鱼中高度复制,增强了基因组稳定性和RNA加工调节能力,有助于避免因冗余DNA增加而引发不稳定性,使得八倍体鲟鱼在生理调控、基因稳定性和环境适应性方面具备更明显的优势。

     

    Abstract: 【Objective】 This study aimed to investigate the phylogenetic relationships and whole-genome duplication (WGD) events across seven sturgeon species, and clarify the characteristics of highly replicated genes in octoploid sturgeons and expansion time of hemoglobin gene family, providing a theoretical basis for revealing genome duplication events and evolutionary strategies of Acipenseriformes.【Method】 Blood samples were collected from three tetraploid sturgeon species (Acipenser stellatusAcipenser ruthenus, and Huso huso) and four octoploid species (Acipenser gueldenstaedtii Acipenser schrenckiiHuso dauricus, and Acipenser sinensis). Draft genomes were constructed using Illumina sequencing data. Gene family expansion and contraction events were analyzed through gene family analysis and phylogenetic tree reconstruction. WGD event timing was estimated based on synonymous substitution rates (Ks) and fourfold degenerate site synonymous codon transversion rates (4DTv). Evolutionary analysis of the hemoglobin gene family was used to infer divergence times. Highly replicated genes that were amplified and retained during octoploidization were screened by comparing genomic coverage depths between octoploid and tetraploid sturgeons. These genes were further analyzed using KEGG signaling pathway enrichment and protein-protein interaction (PPI) networks.【Result】 The seven sturgeon genomes contained a large number of multi-copy orthologs, whereas the number of shared single-copy orthologs was extremely low (only 26). Obvious expansion and contraction events of gene families were observed among sturgeons of different ploidies, with distinct gene retention patterns between tetraploid and octoploid species. Comprehensive analysis of 4DTv and Ks results showed that all sturgeons experienced an ancient Acipenseriformes-specific WGD event (As3R), approximately 118-196 million years ago, coinciding roughly with the period of the Permian-Triassic extinction event. Octoploid sturgeons showed significant differentiation in hemoglobin gene copy numbers: the ratio of α-hemoglobin gene copies was Huso dauricusAcipenser gueldenstaedtiiAcipenser schrenckiiAcipenser sinensis=3∶5∶4∶8, while the ratio for β-hemoglobin was Huso dauricusAcipenser gueldenstaedtiiAcipenser schrenckiiAcipenser sinensis=4∶20∶4∶8. A total of 219 highly replicated genes significantly that expanded and retained in octoploid sturgeons were primarily enriched in pathways related to basal metabolic processes, genomic stability, and expression regulation. The diagram of PPI networks revealed that core genes (PPFIA2ZAP70, and IRG1) played key roles in nervous system development and immune regulation.【Conclusion】 WGD events result in the high replication of genes in signaling pathways such as spliceosomal complex and DNA repair in octoploid sturgeons. This enhances the regulation of genomic stability and RNA processing, helping to avoid instability caused by increased redundant DNA. Consequently, octoploid sturgeon possesses more obvious advantages in physiological regulation, gene stability, and environmental adaptability.

     

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