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利用转录组数据分析高原鼢鼠和裸鼹鼠基因的趋同进化

邓小弓 王堃 张守栋 苏建平 张同作 林恭华   

  1. 中国科学院西北高原生物研究所,中国科学院高原生物适应与进化重点实验室
  • 出版日期:2014-05-13 发布日期:2014-08-18
  • 通讯作者: 张同作zhangtz@nwipb.cas.cn; 林恭华lingonghua@gmail.com
  • 基金资助:
    国家自然科学基金资助项目(31372197,31370405); 中国科学院知识创新工程领域前沿项目(KSCX2 - EW - J -26)

Transcriptomatic determination of convergent evolution between plateau zokors (Eospalax baileyi) and naked mole rats (Heterocephalus glaber)

DENG Xiaogong,WANG Kun,ZHANG Shoudong,SU Jianping,ZHANG Tongzuo,LIN Gonghua   

  1. Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology ,Chinese Academy of Sciences
  • Online:2014-05-13 Published:2014-08-18
  • Contact: ZHANG Tongzuo zhangtz@nwipb.cas.cn; LIN Gonghua lingonghua@gmail.com

摘要: 地下鼠由于长期适应于地下洞道生活,在诸多生物学特征上都产生了一定的趋同进化现象,但目前尚未在分子水平分析其趋同进化特征。本研究利用高通量测序数据,从氨基酸位点变化和基因表达量水平,分析两种亲缘关系较远的地下鼠——高原鼢鼠和裸鼹鼠的趋同进化。氨基酸位点变化分析显示,两种地下鼠的54 个基因都存在至少一个理论趋同进化位点,其中13 个基因可以找到相对明确的表型功能注释。基因表达量分析显示,两种地下鼠在转录组水平的总体表达模式上存在趋同效应;有103 个基因在两种地下鼠脑中的表达量是作为对照的地上鼠(小鼠、豚鼠)表达量的3 倍以上,其中有20 个基因可以找到相对明确的表型功能注释。本研究的结果表明,高原鼢鼠和裸鼹鼠为了适应地下生活方式,在氨基酸序列和基因表达量水平上都产生了一定程度的趋同进化。其中,低氧适应相关基因(氧运输、氧代谢、DNA 修复等)是地下鼠进化适应的最重要组成部分,挖掘器官(尤其是肌肉)功能相关基因的重要性次之,能量代谢及平衡相关基因也是地下鼠适应性进化的关键要素。

关键词: 地下鼠, 趋同进化, 低氧适应, 挖掘器官, 能量代谢

Abstract: Subterranean rodents have evolved convergent traits in many of their biological characteristics that allow them to adapt to a similar underground burrowing life style. However,no study has yet been published about this convergent evolution at the molecular level. Here,we use high-throughput next-generation sequencing data (transcriptomes)to identify both amino acid (AA)variations and gene expression levels in order to analyze the convergent evolution of two typical subterranean rodents,the plateau zokor (Eospalax baileyi)and the naked mole rat (Heterocephalus glaber). AA variation analysis detected 54 genes of which each had at least one convergent adaptation site;of these genes 13 were successfully annotated by their relatively obvious phenotypical functions. Within the 13 genes,four (Ptpn6,Sco1,Dhcr 24,and Add2) were related with hypoxia tolerance or adaptation to oxidative stress,four (Mbtps1,Atp1a1,Acsl3,and Ncoa2)were involved in nutrient transport or energy metabolism,fou(Smoc1,Kif1b, Tcap,and Cryab)were involved in limb development or muscle health,and the remaining gene (Myo6)was involved in auditory function. Gene expression level analyses of the two subterranean rodents detected 103 genes that were significantly upregulated (> 3 fold)as compared to mouse (Mus musculus)and guinea pig (Cavia porcellus);20 of these genes could be successfully annotated by their phenotypical functions. Within these 20 genes,12 were related with hypoxia tolerance functions,such as oxygen transport(Dsg2, Tab2, Hp,Rock1,and F5),oxygen metabolism (Tfb1m and Mrpl1),and DNA repair (Tdp2,Rad50,Alkbh2,Hltf, and Plk1),3 were related with the functional integrity of muscle (Sync and Taf3)and bone (Acp5),and the other 5 were involved in immune (Spon2 and Sh2d4a),biological rhythm (Clock),starvation tolerance (Pdk4 ),and reproduction (Clgn). Our results show that the hypoxia tolerance-related genes were the most important adaptation genes found in the two subterranean rodents,followed by the digging apparatus-related genes (especially the skeletal muscle)in addition to the genes important in energy metabolism and energy balance. This paper provides evidence for convergence of subterranean rodents at the molecular level.

Key words: Convergent evolution, Digging apparatus, Energy metabolism, Hypoxia tolerance, Subterranean rodent