A chromosome-scale reference genome of the Banna miniature inbred pig
Abstract The Banna miniature inbred pig (BN) is an intensively inbred line for biomedical research and xenotransplantation due to its low individual variation and stable genetic background. Although it is originated from the Diannan miniature pig (DN), substantial genetic changes have actually occur...
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Nature Portfolio
2024-12-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-04201-3 |
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| author | Hong-Man Chen Kai-Xiang Xu Chen Yan Heng Zhao De-Ling Jiao Si Si Zheng-Xi Liu Guo-Ying Peng Muhammad Ameen Jamal Min-Juan Lv Pei Wang Yang-Zhi Zeng Hong-Ye Zhao Ming-Shan Wang Hong-Jiang Wei |
| author_facet | Hong-Man Chen Kai-Xiang Xu Chen Yan Heng Zhao De-Ling Jiao Si Si Zheng-Xi Liu Guo-Ying Peng Muhammad Ameen Jamal Min-Juan Lv Pei Wang Yang-Zhi Zeng Hong-Ye Zhao Ming-Shan Wang Hong-Jiang Wei |
| author_sort | Hong-Man Chen |
| collection | DOAJ |
| description | Abstract The Banna miniature inbred pig (BN) is an intensively inbred line for biomedical research and xenotransplantation due to its low individual variation and stable genetic background. Although it is originated from the Diannan miniature pig (DN), substantial genetic changes have actually occurred. However, the lack of a BN reference genome has limited studies on the complete genomic architecture and utilization as a biomedical model. Here, we present a high-quality genome for BN using PacBio HiFi and Hi-C sequencing technologies, with a total length of 2.66 Gb, a scaffold N50 of 143.60 Mb, and 97.59% of the sequences anchored to chromosomes. Its BUSCO score is 96.30%, higher than porcine reference assembly and DN. The genome contains 48.49% of repeats, 19,756 protein-coding genes, and 7,207 non-coding RNAs according to our annotation. The OMArk score shows a proteome completeness and consistency of 99.58% and 93.62%, respectively. These findings indicate that the chromosome-scale genome of BN provides a valuable resource for studying the genetic basis of inbreeding, facilitating further research and clinical applications. |
| format | Article |
| id | doaj-art-2ed5006e7bb74fc5a4cd502fc31597fa |
| institution | OA Journals |
| issn | 2052-4463 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-2ed5006e7bb74fc5a4cd502fc31597fa2025-08-20T01:57:15ZengNature PortfolioScientific Data2052-44632024-12-0111111010.1038/s41597-024-04201-3A chromosome-scale reference genome of the Banna miniature inbred pigHong-Man Chen0Kai-Xiang Xu1Chen Yan2Heng Zhao3De-Ling Jiao4Si Si5Zheng-Xi Liu6Guo-Ying Peng7Muhammad Ameen Jamal8Min-Juan Lv9Pei Wang10Yang-Zhi Zeng11Hong-Ye Zhao12Ming-Shan Wang13Hong-Jiang Wei14Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityKey Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityKey Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKey Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityKey Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural UniversityAbstract The Banna miniature inbred pig (BN) is an intensively inbred line for biomedical research and xenotransplantation due to its low individual variation and stable genetic background. Although it is originated from the Diannan miniature pig (DN), substantial genetic changes have actually occurred. However, the lack of a BN reference genome has limited studies on the complete genomic architecture and utilization as a biomedical model. Here, we present a high-quality genome for BN using PacBio HiFi and Hi-C sequencing technologies, with a total length of 2.66 Gb, a scaffold N50 of 143.60 Mb, and 97.59% of the sequences anchored to chromosomes. Its BUSCO score is 96.30%, higher than porcine reference assembly and DN. The genome contains 48.49% of repeats, 19,756 protein-coding genes, and 7,207 non-coding RNAs according to our annotation. The OMArk score shows a proteome completeness and consistency of 99.58% and 93.62%, respectively. These findings indicate that the chromosome-scale genome of BN provides a valuable resource for studying the genetic basis of inbreeding, facilitating further research and clinical applications.https://doi.org/10.1038/s41597-024-04201-3 |
| spellingShingle | Hong-Man Chen Kai-Xiang Xu Chen Yan Heng Zhao De-Ling Jiao Si Si Zheng-Xi Liu Guo-Ying Peng Muhammad Ameen Jamal Min-Juan Lv Pei Wang Yang-Zhi Zeng Hong-Ye Zhao Ming-Shan Wang Hong-Jiang Wei A chromosome-scale reference genome of the Banna miniature inbred pig Scientific Data |
| title | A chromosome-scale reference genome of the Banna miniature inbred pig |
| title_full | A chromosome-scale reference genome of the Banna miniature inbred pig |
| title_fullStr | A chromosome-scale reference genome of the Banna miniature inbred pig |
| title_full_unstemmed | A chromosome-scale reference genome of the Banna miniature inbred pig |
| title_short | A chromosome-scale reference genome of the Banna miniature inbred pig |
| title_sort | chromosome scale reference genome of the banna miniature inbred pig |
| url | https://doi.org/10.1038/s41597-024-04201-3 |
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