Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals
Summary: Subterranean mammals exhibit diverse traits for underground life, making them ideal models for studying molecular mechanisms of adaptation and convergence in extreme environments. To investigate these processes at both the genomic and gut microbiome levels, we assemble a chromosome-level ge...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-08-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124725008812 |
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| author | Kexin Li Yixin Liu Yehao Zhang Zhenxin Fan Xiangxu Hu Xinlei Lai Fuwen Wei Yibo Hu |
| author_facet | Kexin Li Yixin Liu Yehao Zhang Zhenxin Fan Xiangxu Hu Xinlei Lai Fuwen Wei Yibo Hu |
| author_sort | Kexin Li |
| collection | DOAJ |
| description | Summary: Subterranean mammals exhibit diverse traits for underground life, making them ideal models for studying molecular mechanisms of adaptation and convergence in extreme environments. To investigate these processes at both the genomic and gut microbiome levels, we assemble a chromosome-level genome of the Chinese bamboo rat (Rhizomys sinensis) and identify an expansion of the Hsp90 gene family, potentially associated with hypoxia adaptation. Transcriptomic analysis reveals gene expression changes related to tooth development and visual perception in the Chinese bamboo rat. Furthermore, we identify convergent genetic changes related to vision, hearing, immunity, and hypoxia among subterranean mammals, with widespread Krt9 pseudogenization potentially linked to long-term burrowing behavior. However, the gut microbiome shows no structural or functional convergence in subterranean mammals, being shaped by host phylogeny and gut morphology rather than habitat. These findings suggest that host genomic rather than gut microbiome convergence underlies convergent subterranean adaptation, offering multi-omics insights into subterranean adaptation. |
| format | Article |
| id | doaj-art-7d272d43e2a8496f89bb2bf57c6a1f06 |
| institution | Kabale University |
| issn | 2211-1247 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj-art-7d272d43e2a8496f89bb2bf57c6a1f062025-08-20T03:36:22ZengElsevierCell Reports2211-12472025-08-0144811611010.1016/j.celrep.2025.116110Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammalsKexin Li0Yixin Liu1Yehao Zhang2Zhenxin Fan3Xiangxu Hu4Xinlei Lai5Fuwen Wei6Yibo Hu7State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaState Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaState Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaKey Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, ChinaState Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaState Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaState Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Jiangxi Province Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; Corresponding authorState Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Corresponding authorSummary: Subterranean mammals exhibit diverse traits for underground life, making them ideal models for studying molecular mechanisms of adaptation and convergence in extreme environments. To investigate these processes at both the genomic and gut microbiome levels, we assemble a chromosome-level genome of the Chinese bamboo rat (Rhizomys sinensis) and identify an expansion of the Hsp90 gene family, potentially associated with hypoxia adaptation. Transcriptomic analysis reveals gene expression changes related to tooth development and visual perception in the Chinese bamboo rat. Furthermore, we identify convergent genetic changes related to vision, hearing, immunity, and hypoxia among subterranean mammals, with widespread Krt9 pseudogenization potentially linked to long-term burrowing behavior. However, the gut microbiome shows no structural or functional convergence in subterranean mammals, being shaped by host phylogeny and gut morphology rather than habitat. These findings suggest that host genomic rather than gut microbiome convergence underlies convergent subterranean adaptation, offering multi-omics insights into subterranean adaptation.http://www.sciencedirect.com/science/article/pii/S2211124725008812CP: Genomics |
| spellingShingle | Kexin Li Yixin Liu Yehao Zhang Zhenxin Fan Xiangxu Hu Xinlei Lai Fuwen Wei Yibo Hu Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals Cell Reports CP: Genomics |
| title | Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals |
| title_full | Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals |
| title_fullStr | Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals |
| title_full_unstemmed | Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals |
| title_short | Host genomic convergence, rather than gut microbiome convergence, underlies the convergent evolution of subterranean adaptation in mammals |
| title_sort | host genomic convergence rather than gut microbiome convergence underlies the convergent evolution of subterranean adaptation in mammals |
| topic | CP: Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2211124725008812 |
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