Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species
Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover...
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Frontiers Media S.A.
2024-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/full |
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| author | Jiarui Chen Jiarui Chen Shuwen Wang Dong Wang Dong Wang Yunkang Chiu Nan Yang Xinming Lian Xinming Lian Zicheng Zhao Qing Wei Qing Wei |
| author_facet | Jiarui Chen Jiarui Chen Shuwen Wang Dong Wang Dong Wang Yunkang Chiu Nan Yang Xinming Lian Xinming Lian Zicheng Zhao Qing Wei Qing Wei |
| author_sort | Jiarui Chen |
| collection | DOAJ |
| description | Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope.Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples.Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope.Discussion: This effort enhances our comprehension of the genomic landscape of this species. |
| first_indexed | 2024-03-08T00:50:09Z |
| format | Article |
| id | doaj.art-9c34533ad6de4229ac9a7695e0e47309 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-08T00:50:09Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-9c34533ad6de4229ac9a7695e0e473092024-02-15T05:11:12ZengFrontiers Media S.A.Frontiers in Genetics1664-80212024-02-011510.3389/fgene.2024.13025541302554Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous speciesJiarui Chen0Jiarui Chen1Shuwen Wang2Dong Wang3Dong Wang4Yunkang Chiu5Nan Yang6Xinming Lian7Xinming Lian8Zicheng Zhao9Qing Wei10Qing Wei11College of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, ChinaState Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, ChinaCollege of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, ChinaKey Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, ChinaSchool of Geographical Science, Qinghai Normal University, Xining, Qinghai, ChinaShenzhen Byoryn Technology Co., Ltd., Shenzhen, ChinaNational Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, ChinaQinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, ChinaShenzhen Byoryn Technology Co., Ltd., Shenzhen, ChinaCollege of Eco‐Environmental Engineering, Qinghai University, Xining, Qinghai, ChinaState Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, ChinaIntroduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope.Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples.Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope.Discussion: This effort enhances our comprehension of the genomic landscape of this species.https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/fullTibetan antelopegenome refinementgenome comparisongenome rearrangementslinkage disequilibrium |
| spellingShingle | Jiarui Chen Jiarui Chen Shuwen Wang Dong Wang Dong Wang Yunkang Chiu Nan Yang Xinming Lian Xinming Lian Zicheng Zhao Qing Wei Qing Wei Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species Frontiers in Genetics Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium |
| title | Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species |
| title_full | Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species |
| title_fullStr | Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species |
| title_full_unstemmed | Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species |
| title_short | Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species |
| title_sort | uncovering rearrangements in the tibetan antelope via population derived genome refinement and comparative analysis with homologous species |
| topic | Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/full |
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