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Background <p>Mammals exhibit diverse adaptations to varied habitats, yet the genomic mechanisms underlying these transitions remain incompletely understood. Here, we present a comparative genomic, epigenomic, and three-dimensional chromatin analysis of two closely related zokor species, <i>Myospalax aspalax</i> and <i>Myospalax psilurus</i>, which inhabit arid and humid subterranean environments, respectively.</p> Results <p>We identified subterranean lineage-specific positively selected and rapidly evolving genes enriched for DNA repair, hypoxia response, blood vessel development, and fructose metabolism. <i>M. psilurus</i> showed a notable loss of olfactory receptor genes, expansion of pheromone-related gene families, and widespread activation of a specific ERVK transposable element family, accompanied by elevated DNA methylation, suggesting enhanced epigenetic defenses and ecological specialization. In contrast, <i>M. aspalax</i> showed selection in kidney and lipid metabolism genes. Large chromosomal inversions (&gt; 1&#xa0;Mb) overlapped islands of high genetic divergence (high-<i>F</i><sub>ST</sub> or high <i>D</i><sub>xy</sub>) and were enriched for sensory, reproductive, and DNA repair genes. Although chromatin compartments remained largely stable, large inversions disrupted topologically associating domains and preferentially occurred in regions characterized by longer chromatin loops. Inversion breakpoints were flanked by inverted repeats and segmental duplications—features characteristic of the formation mechanism of non-allelic homologous recombination, suggesting that both the spatial proximity and sequence architecture of these regions may predispose them to large inversions.</p> Conclusions <p>Overall, our results illuminate the structural, regulatory, and evolutionary mechanisms underlying ecological divergence and highlight how genome architecture contributes to adaptive evolution in subterranean mammals.</p>

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Genomic signatures of subterranean lifestyle and ecological adaptation in Myospalax

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月3日

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  • Na Wan,
  • Jiaqi Chen,
  • Muli Jiang,
  • Mengzhuo Wu,
  • Haolin Li,
  • Mozhi Wen,
  • Wei Shen,
  • Xiaolong Liang,
  • Xiaojie Yang,
  • Yijing Liu,
  • Yige Gao,
  • Eviatar Nevo,
  • Kexin Li

摘要

Background

Mammals exhibit diverse adaptations to varied habitats, yet the genomic mechanisms underlying these transitions remain incompletely understood. Here, we present a comparative genomic, epigenomic, and three-dimensional chromatin analysis of two closely related zokor species, Myospalax aspalax and Myospalax psilurus, which inhabit arid and humid subterranean environments, respectively.

Results

We identified subterranean lineage-specific positively selected and rapidly evolving genes enriched for DNA repair, hypoxia response, blood vessel development, and fructose metabolism. M. psilurus showed a notable loss of olfactory receptor genes, expansion of pheromone-related gene families, and widespread activation of a specific ERVK transposable element family, accompanied by elevated DNA methylation, suggesting enhanced epigenetic defenses and ecological specialization. In contrast, M. aspalax showed selection in kidney and lipid metabolism genes. Large chromosomal inversions (> 1 Mb) overlapped islands of high genetic divergence (high-FST or high Dxy) and were enriched for sensory, reproductive, and DNA repair genes. Although chromatin compartments remained largely stable, large inversions disrupted topologically associating domains and preferentially occurred in regions characterized by longer chromatin loops. Inversion breakpoints were flanked by inverted repeats and segmental duplications—features characteristic of the formation mechanism of non-allelic homologous recombination, suggesting that both the spatial proximity and sequence architecture of these regions may predispose them to large inversions.

Conclusions

Overall, our results illuminate the structural, regulatory, and evolutionary mechanisms underlying ecological divergence and highlight how genome architecture contributes to adaptive evolution in subterranean mammals.