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郭媛婷, 张佳, 许东明, 唐利洲, 刘振. 2021: 鼹形鼠科基于基因组的系统发生关系与适应地下生活的分子趋同分析. 动物学研究, 42(5): 671-674. DOI: 10.24272/j.issn.2095-8137.2021.240
引用本文: 郭媛婷, 张佳, 许东明, 唐利洲, 刘振. 2021: 鼹形鼠科基于基因组的系统发生关系与适应地下生活的分子趋同分析. 动物学研究, 42(5): 671-674. DOI: 10.24272/j.issn.2095-8137.2021.240
Yuan-Ting Guo, Jia Zhang, Dong-Ming Xu, Li-Zhou Tang, Zhen Liu. 2021: Phylogenomic relationships and molecular convergences to subterranean life in rodent family Spalacidae. Zoological Research, 42(5): 671-674. DOI: 10.24272/j.issn.2095-8137.2021.240
Citation: Yuan-Ting Guo, Jia Zhang, Dong-Ming Xu, Li-Zhou Tang, Zhen Liu. 2021: Phylogenomic relationships and molecular convergences to subterranean life in rodent family Spalacidae. Zoological Research, 42(5): 671-674. DOI: 10.24272/j.issn.2095-8137.2021.240

鼹形鼠科基于基因组的系统发生关系与适应地下生活的分子趋同分析

Phylogenomic relationships and molecular convergences to subterranean life in rodent family Spalacidae

  • 摘要: 啮齿目鼹形鼠科(Spalacidae)的所有物种都是地下生活的,演化出了多样的营地下生活的特征。然而,该科中三个亚科(Myospalacinae、Smalacinae和Rhizomyinae)间的系统发生关系及其适应地下生活的分子基础仍然知之甚少。该研究对银星竹鼠(Rhizomys pruinosus)进行了全基因组测序及组装,解析了鼹形鼠科三个亚科之间的系统发生关系。研究表明,在11028个一对一直系同源蛋白编码基因中,约50%支持Myospalacinae和Rhizomyinae亲缘关系更近。基于这些同源基因串联序列的系统发生分析也强力支持该结果。进一步的分析发现,鼹形鼠科的三个亚科是在一个相对较短的时间跨度下分化出来的(~200万年)。与具有相似分化时间的非地下对照组相比,鼹形鼠科与非洲鼹鼠存在显著多的趋同基因,这些趋同基因在单羧酸生物合成过程、羧酸转运、血管形态发生和氧化应激反应等功能类别中富集,提示着它们可能参与到了鼹形鼠科适应低O2–高CO2的地下环境的演化过程中。该研究不仅揭示了鼹形鼠科三个亚科之间系统发生关系,而且探讨了鼹形鼠科营地下生活的分子适应机制。

     

    Abstract: All extant species in the rodent family Spalacidae are subterranean and have evolved various traits for underground life. However, the phylogenomic relationships among its three subfamilies (Myospalacinae, Spalacinae, and Rhizomyinae) and the molecular basis underlying their adaptations to underground life remain poorly understood. Here, we inferred the phylogenomic relationships among these subfamilies based on de novo sequencing the genome of the hoary bamboo rat (Rhizomys pruinosus). Analyses showed that ~50% of the identified 11 028 one-to-one orthologous protein-coding genes and the concatenated sequences of these orthologous genes strongly supported a sister relationship between Myospalacinae and Rhizomyinae. The three subfamilies diversified from each other within ~2 million years. Compared with the non-subterranean controls with similar divergence dates, the spalacids shared more convergent genes with the African subterranean mole-rats at the genomic scale due to more rapid protein sequence evolution. Furthermore, these convergent genes were enriched in the functional categories of carboxylic acid transport, vascular morphogenesis, and response to oxidative stress, which are closely associated with adaptations to the hypoxic-hypercapnic underground environment. Our study presents a well-supported phylogenomic relationship among the three subfamilies of Spalacidae and offers new insights into the molecular adaptations of spalacids living underground.

     

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