A chromosome-scale reference genome of the Banna miniature inbred pig

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

doi:10.1038/s41597-024-04201-3

A chromosome-scale reference genome of the Banna miniature inbred pig

Sci Data. 2024 Dec 18;11(1):1345. doi: 10.1038/s41597-024-04201-3.

Authors

Hong-Man Chen^#^{1

2

3}, Kai-Xiang Xu^#^{1

3}, Chen Yan⁴, Heng Zhao^{1

3}, De-Ling Jiao^{1

3}, Si Si⁴, Zheng-Xi Liu⁴, Guo-Ying Peng^{1

2}, Muhammad Ameen Jamal^{1

4}, Min-Juan Lv^{1

2}, Pei Wang^{1

3}, Yang-Zhi Zeng¹, Hong-Ye Zhao^{5

6}, Ming-Shan Wang^{7

8}, Hong-Jiang Wei^{9

10

11

12}

Affiliations

¹ Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
² Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
³ College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
⁴ Key Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
⁵ Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China. [email protected].
⁶ College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China. [email protected].
⁷ Key Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. [email protected].
⁸ Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. [email protected].
⁹ Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China. [email protected].
¹⁰ Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China. [email protected].
¹¹ College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China. [email protected].
¹² Key Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. [email protected].

^# Contributed equally.

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.

Publication types

Dataset

MeSH terms

Animals
Genome*
Inbreeding
Swine / genetics
Swine, Miniature* / genetics

Abstract

Publication types

MeSH terms

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