The sequence and analysis of a Chinese pig genome

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.

Figure 1

Heterozygosis distribution of WZSP, naked mole rat, inbred mouse at F280 and human using a 50 Kbp non-overlapping sliding window. WZSP and inbred mouse show a large amount of a low heterozygosis region (59.97% and 69.15% of the windows respectively for heterozygosis ratio < 0.01%).

Figure 2

Divergence distribution of SINE/tRNA in the pig genome. (A) The divergence distribution of all SINE/tRNA, and (B) the divergence distribution of classified SINE/tRNA subfamilies.

Figure 3

Estimation of divergence time. The time of divergence (with error range shown in parentheses) of pig and seven other mammals based on orthology relationships. Distances are shown in millions of years.

Figure 4

PERVs in the WZSP genome. (A) Distribution of similarity between virus protein and its counterpart in WZSP genome by considering factors of sequence identity and coverage. (B) Structure of whole PERV genome inserted into the pig genome. The upper panel shows the sequencing depth of the assembled scaffold. The middle panel visualizes the paired-end alignment of the scaffold providing evidence of correct assembly. The bottom panel shows the genome structure of PERV and its integration site in the scaffold.