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The sequence and analysis of a Chinese pig genome

Xiaodong Fang1, Yulian Mou2, Zhiyong Huang1, Yong Li134, Lijuan Han1, Yanfeng Zhang5, Yue Feng1, Yuanxin Chen1, Xuanting Jiang1, Wei Zhao1, Xiaoqing Sun1, Zhiqiang Xiong1, Lan Yang1, Huan Liu134, Dingding Fan1, Likai Mao1, Lijie Ren6, Chuxin Liu134, Juan Wang1, Kui Li2, Guangbiao Wang1, Shulin Yang2, Liangxue Lai7, Guojie Zhang1, Yingrui Li1, Jun Wang189, Lars Bolund110, Huanming Yang1, Jian Wang1, Shutang Feng2*, Songgang Li1* and Yutao Du134*

Author Affiliations

1 BGI-Shenzhen, Bei Shan Road, Yantian, Shenzhen, 518083, China

2 Institute of Animal Science (IAS), Chinese Academy of Agriculture Science (CAAS), Beijing, 10094, China

3 Shenzhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Bei Shan Road, Yantian, Shenzhen, 518083, China

4 BGI Ark Biotechnology (BAB), Bei Shan Road, Yantian, Shenzhen, 518083, China

5 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China

6 Department of Neurology, Shenzhen Second People’s Hospital (First Affiliated Hospital of Shenzhen University), Shenzhen, 518035, China

7 Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangdong, China

8 Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark

9 Department of Biology, University of Copenhagen, Copenhagen, Denmark

10 Department of Biomedicine, Aarhus University, Aarhus C, Denmark

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GigaScience 2012, 1:16  doi:10.1186/2047-217X-1-16

Published: 15 November 2012

Abstract

Background

The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP), as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome.

Results

Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes.

Conclusion

Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models.

Keywords:
Wuzhishan pig; Genome; Homozygosis; Transposable element; Endogenous retrovirus; Animal model