State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.
Zool Res. 2021 Sep 18;42(5):671-674. doi: 10.24272/j.issn.2095-8137.2021.240.
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 sequencing the genome of the hoary bamboo rat ( ). 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.
所有现存的沙鼠科物种都是穴居的，它们为地下生活进化出了各种特征。然而，其三个亚科（Myospalacinae、Spalacinae 和 Rhizomyinae）之间的系统发育关系以及它们适应地下生活的分子基础仍知之甚少。在这里，我们基于对蓬尾沙鼠（）基因组的测序，推断了这些亚科之间的系统发育关系。分析表明，在鉴定的 11028 个一对一的直系同源蛋白编码基因中，约有 50%和这些直系同源基因的串联序列强烈支持 Myospalacinae 和 Rhizomyinae 是姐妹关系。这三个亚科在 200 万年内彼此分化。与具有相似分化日期的非穴居对照相比，由于蛋白质序列进化更快，沙鼠科与非洲穴居的鼹形田鼠在基因组水平上共享了更多与适应缺氧高碳酸地下环境相关的趋同基因。此外，这些趋同基因在羧酸转运、血管形态发生和应对氧化应激的功能类别中富集，这些功能类别与适应缺氧高碳酸地下环境密切相关。我们的研究提供了沙鼠科三个亚科之间强有力的系统发育关系，并为地下生活的沙鼠科的分子适应提供了新的见解。
