Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs
© 2023 The Authors..
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:26 |
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| Enthalten in: |
iScience - 26(2023), 3 vom: 17. März, Seite 106119 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Jiang, Yi-Fan [VerfasserIn] |
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| Anmerkungen: |
Date Revised 27.04.2024 published: Electronic-eCollection Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1016/j.isci.2023.106119 |
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| Förderinstitution / Projekttitel: |
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| 520 | |a Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs | ||
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| 650 | 4 | |a Phylogenetics | |
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| 700 | 1 | |a Wang, Chong-Long |e verfasserin |4 aut | |
| 700 | 1 | |a Xu, Ru-Hai |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Wen-Wen |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Yao |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Ming-Shan |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Li |e verfasserin |4 aut | |
| 700 | 1 | |a Dai, Li-He |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Jie-Ru |e verfasserin |4 aut | |
| 700 | 1 | |a Chu, Xiao-Hong |e verfasserin |4 aut | |
| 700 | 1 | |a Zeng, Yong-Qing |e verfasserin |4 aut | |
| 700 | 1 | |a Fang, Ling-Zhao |e verfasserin |4 aut | |
| 700 | 1 | |a Wu, Dong-Dong |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Qin |e verfasserin |4 aut | |
| 700 | 1 | |a Ding, Xiang-Dong |e verfasserin |4 aut | |
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