Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon
Abstract Background Neodon, a typical group of high-altitude rodents, originated in the high-altitude regions of the Tibet-Himalayan area. These rodents inhabit meadows, swampy grasslands, and shrublands at elevations ranging from 3,700 to 4,800 m in Qinghai-Tibet Plateau, where they experience envi...
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2025-06-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11709-4 |
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| author | Peng Yang Jiapeng Qu Yingxu Wang Zhongshi Xu Tuo Feng Gang Chang Lulu Xu Rong Dong Da Mi Yandong Ren Gang Li Ting Sun |
| author_facet | Peng Yang Jiapeng Qu Yingxu Wang Zhongshi Xu Tuo Feng Gang Chang Lulu Xu Rong Dong Da Mi Yandong Ren Gang Li Ting Sun |
| author_sort | Peng Yang |
| collection | DOAJ |
| description | Abstract Background Neodon, a typical group of high-altitude rodents, originated in the high-altitude regions of the Tibet-Himalayan area. These rodents inhabit meadows, swampy grasslands, and shrublands at elevations ranging from 3,700 to 4,800 m in Qinghai-Tibet Plateau, where they experience environment stresses such as hypoxia, enhanced ultraviolet radiation, and low temperature. Results In this study, we assembled a high-quality chromosome-level genome of Neodon fuscus and use it to investigate the potential genetic bases of high-altitude adaptation. The genome of N. fuscus shows gene family expansion in genes related to immunity. Comparative genomics analysis revealed several positively selected genes and rapidly evolving genes associated with DNA damage repair (Atm and Pdia4) and male sperm quality (Idh3b and Atplb1) that aid in clarifying high-altitude adaptation of Neodon species. Additionally, we found that genes (Nrp2, Vav3, Cat and Adam8) associated with oxidative stress and cardiovascular regulation seem to have experienced convergent evolution among plateau species. Notably, we identified a Neodon-specific 24 bp deletion in Map3k6, which may regulate angiogenesis, aiding Neodon species adapt to hypoxic environments. Conclusion These findings elucidate molecular mechanisms underlying high-altitude adaptation, emphasizing the integrative roles of immunity, stress response, and reproduction. The high-quality genome of N. fuscus offers new insights into how Neodon adapt to high-altitude environments and will facilitate future research on Neodon. |
| format | Article |
| id | doaj-art-65e4e3035b27494fbbf9763ead258555 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-65e4e3035b27494fbbf9763ead2585552025-08-20T03:25:16ZengBMCBMC Genomics1471-21642025-06-0126111510.1186/s12864-025-11709-4Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and NeodonPeng Yang0Jiapeng Qu1Yingxu Wang2Zhongshi Xu3Tuo Feng4Gang Chang5Lulu Xu6Rong Dong7Da Mi8Yandong Ren9Gang Li10Ting Sun11College of Life Sciences, Shaanxi Normal UniversityKey Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesCollege of Life Sciences, Shaanxi Normal UniversityCollege of Life Sciences, Shaanxi Normal UniversityShaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of ZoologyShaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of ZoologyCollege of Life Sciences, Shaanxi Normal UniversityResearch Center for Qinling Giant Panda, Shaanxi Academy of ForestryXi’an Haorui Genomics Technology Co., LtdCollege of Life Sciences, Shaanxi Normal UniversityCollege of Life Sciences, Shaanxi Normal UniversityCollege of Life Sciences, Shaanxi Normal UniversityAbstract Background Neodon, a typical group of high-altitude rodents, originated in the high-altitude regions of the Tibet-Himalayan area. These rodents inhabit meadows, swampy grasslands, and shrublands at elevations ranging from 3,700 to 4,800 m in Qinghai-Tibet Plateau, where they experience environment stresses such as hypoxia, enhanced ultraviolet radiation, and low temperature. Results In this study, we assembled a high-quality chromosome-level genome of Neodon fuscus and use it to investigate the potential genetic bases of high-altitude adaptation. The genome of N. fuscus shows gene family expansion in genes related to immunity. Comparative genomics analysis revealed several positively selected genes and rapidly evolving genes associated with DNA damage repair (Atm and Pdia4) and male sperm quality (Idh3b and Atplb1) that aid in clarifying high-altitude adaptation of Neodon species. Additionally, we found that genes (Nrp2, Vav3, Cat and Adam8) associated with oxidative stress and cardiovascular regulation seem to have experienced convergent evolution among plateau species. Notably, we identified a Neodon-specific 24 bp deletion in Map3k6, which may regulate angiogenesis, aiding Neodon species adapt to hypoxic environments. Conclusion These findings elucidate molecular mechanisms underlying high-altitude adaptation, emphasizing the integrative roles of immunity, stress response, and reproduction. The high-quality genome of N. fuscus offers new insights into how Neodon adapt to high-altitude environments and will facilitate future research on Neodon.https://doi.org/10.1186/s12864-025-11709-4High-altitude adaptationReference-quality genomeComparative genomicsNeodon |
| spellingShingle | Peng Yang Jiapeng Qu Yingxu Wang Zhongshi Xu Tuo Feng Gang Chang Lulu Xu Rong Dong Da Mi Yandong Ren Gang Li Ting Sun Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon BMC Genomics High-altitude adaptation Reference-quality genome Comparative genomics Neodon |
| title | Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon |
| title_full | Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon |
| title_fullStr | Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon |
| title_full_unstemmed | Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon |
| title_short | Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon |
| title_sort | chromosome level genome of neodon fuscus sheds light on the evolution and plateau adaptation of n fuscus and neodon |
| topic | High-altitude adaptation Reference-quality genome Comparative genomics Neodon |
| url | https://doi.org/10.1186/s12864-025-11709-4 |
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