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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Autor*in:	Jiarui Chen [verfasserIn] Shuwen Wang [verfasserIn] Dong Wang [verfasserIn] Yunkang Chiu [verfasserIn] Nan Yang [verfasserIn] Xinming Lian [verfasserIn] Zicheng Zhao [verfasserIn] Qing Wei [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2024

Schlagwörter:	Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium

Übergeordnetes Werk:	In: Frontiers in Genetics - Frontiers Media S.A., 2011, 15(2024)
Übergeordnetes Werk:	volume:15 ; year:2024

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fgene.2024.1302554

Katalog-ID:	DOAJ101626029

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520			\|a 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.
650		4	\|a Tibetan antelope
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allfields	10.3389/fgene.2024.1302554 doi (DE-627)DOAJ101626029 (DE-599)DOAJ9c34533ad6de4229ac9a7695e0e47309 DE-627 ger DE-627 rakwb eng QH426-470 Jiarui Chen verfasserin aut Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium Genetics Jiarui Chen verfasserin aut Shuwen Wang verfasserin aut Dong Wang verfasserin aut Dong Wang verfasserin aut Yunkang Chiu verfasserin aut Nan Yang verfasserin aut Xinming Lian verfasserin aut Xinming Lian verfasserin aut Zicheng Zhao verfasserin aut Qing Wei verfasserin aut Qing Wei verfasserin aut In Frontiers in Genetics Frontiers Media S.A., 2011 15(2024) (DE-627)65799829X (DE-600)2606823-0 16648021 nnns volume:15 year:2024 https://doi.org/10.3389/fgene.2024.1302554 kostenfrei https://doaj.org/article/9c34533ad6de4229ac9a7695e0e47309 kostenfrei https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/full kostenfrei https://doaj.org/toc/1664-8021 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
spelling	10.3389/fgene.2024.1302554 doi (DE-627)DOAJ101626029 (DE-599)DOAJ9c34533ad6de4229ac9a7695e0e47309 DE-627 ger DE-627 rakwb eng QH426-470 Jiarui Chen verfasserin aut Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium Genetics Jiarui Chen verfasserin aut Shuwen Wang verfasserin aut Dong Wang verfasserin aut Dong Wang verfasserin aut Yunkang Chiu verfasserin aut Nan Yang verfasserin aut Xinming Lian verfasserin aut Xinming Lian verfasserin aut Zicheng Zhao verfasserin aut Qing Wei verfasserin aut Qing Wei verfasserin aut In Frontiers in Genetics Frontiers Media S.A., 2011 15(2024) (DE-627)65799829X (DE-600)2606823-0 16648021 nnns volume:15 year:2024 https://doi.org/10.3389/fgene.2024.1302554 kostenfrei https://doaj.org/article/9c34533ad6de4229ac9a7695e0e47309 kostenfrei https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/full kostenfrei https://doaj.org/toc/1664-8021 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
allfields_unstemmed	10.3389/fgene.2024.1302554 doi (DE-627)DOAJ101626029 (DE-599)DOAJ9c34533ad6de4229ac9a7695e0e47309 DE-627 ger DE-627 rakwb eng QH426-470 Jiarui Chen verfasserin aut Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium Genetics Jiarui Chen verfasserin aut Shuwen Wang verfasserin aut Dong Wang verfasserin aut Dong Wang verfasserin aut Yunkang Chiu verfasserin aut Nan Yang verfasserin aut Xinming Lian verfasserin aut Xinming Lian verfasserin aut Zicheng Zhao verfasserin aut Qing Wei verfasserin aut Qing Wei verfasserin aut In Frontiers in Genetics Frontiers Media S.A., 2011 15(2024) (DE-627)65799829X (DE-600)2606823-0 16648021 nnns volume:15 year:2024 https://doi.org/10.3389/fgene.2024.1302554 kostenfrei https://doaj.org/article/9c34533ad6de4229ac9a7695e0e47309 kostenfrei https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/full kostenfrei https://doaj.org/toc/1664-8021 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
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allfieldsSound	10.3389/fgene.2024.1302554 doi (DE-627)DOAJ101626029 (DE-599)DOAJ9c34533ad6de4229ac9a7695e0e47309 DE-627 ger DE-627 rakwb eng QH426-470 Jiarui Chen verfasserin aut Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium Genetics Jiarui Chen verfasserin aut Shuwen Wang verfasserin aut Dong Wang verfasserin aut Dong Wang verfasserin aut Yunkang Chiu verfasserin aut Nan Yang verfasserin aut Xinming Lian verfasserin aut Xinming Lian verfasserin aut Zicheng Zhao verfasserin aut Qing Wei verfasserin aut Qing Wei verfasserin aut In Frontiers in Genetics Frontiers Media S.A., 2011 15(2024) (DE-627)65799829X (DE-600)2606823-0 16648021 nnns volume:15 year:2024 https://doi.org/10.3389/fgene.2024.1302554 kostenfrei https://doaj.org/article/9c34533ad6de4229ac9a7695e0e47309 kostenfrei https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/full kostenfrei https://doaj.org/toc/1664-8021 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2024
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callnumber-first	Q - Science
author	Jiarui Chen
spellingShingle	Jiarui Chen misc QH426-470 misc Tibetan antelope misc genome refinement misc genome comparison misc genome rearrangements misc linkage disequilibrium misc Genetics Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species
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topic_title	QH426-470 Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species Tibetan antelope genome refinement genome comparison genome rearrangements linkage disequilibrium
topic	misc QH426-470 misc Tibetan antelope misc genome refinement misc genome comparison misc genome rearrangements misc linkage disequilibrium misc Genetics
topic_unstemmed	misc QH426-470 misc Tibetan antelope misc genome refinement misc genome comparison misc genome rearrangements misc linkage disequilibrium misc Genetics
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title	Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species
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title_full	Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species
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title_sort	uncovering rearrangements in the tibetan antelope via population-derived genome refinement and comparative analysis with homologous species
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title_auth	Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species
url	https://doi.org/10.3389/fgene.2024.1302554 https://doaj.org/article/9c34533ad6de4229ac9a7695e0e47309 https://www.frontiersin.org/articles/10.3389/fgene.2024.1302554/full https://doaj.org/toc/1664-8021
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Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species

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