Comprehensive inbred variation discovery in Bama pigs using de novo assemblies

Li Zhang; Yuemeng Huang; Jinglei Si; Yanjun Wu; Meng Wang; Qinyang Jiang; Yafen Guo; Jing Liang; Ganqiu Lan

doi:10.1016/j.gene.2018.08.051

Comprehensive inbred variation discovery in Bama pigs using de novo assemblies

Gene. 2018 Dec 30:679:81-89. doi: 10.1016/j.gene.2018.08.051. Epub 2018 Sep 1.

Authors

Li Zhang¹, Yuemeng Huang², Jinglei Si¹, Yanjun Wu¹, Meng Wang³, Qinyang Jiang¹, Yafen Guo¹, Jing Liang⁴, Ganqiu Lan⁵

Affiliations

¹ College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
² College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China.
³ Novogene Bioinformatics Institute, Beijing 100083, China.
⁴ College of Animal Science and Technology, Guangxi University, Nanning 530004, China. Electronic address: liangjing@gxu.edu.cn.
⁵ College of Animal Science and Technology, Guangxi University, Nanning 530004, China. Electronic address: gqlan@gxu.edu.cn.

PMID: 30179680
DOI: 10.1016/j.gene.2018.08.051

Abstract

The Bama mini-pig (BM pig) is an inbred strain of the Bama Xiang pig (BX pig) and an important animal model used for studying human diseases. The extremely long inbreeding period renders a clear distinction between the features of the BM and BX strains, such as in their metabolism and olfactory system. However, there is limited information about differences between BM and BX animals at the genomic level. In this study, we generated genome sequencing data and used the assembly-vs-assembly approach to evaluate the phenotypic variations caused by inbreeding in these strains. Moreover, we detected differential expression of mutant genes related to the phenotypes in BX and BM pigs. We sequenced the genome of the BX pig strain and performed a series of analyses to reveal the comprehensive inbred genetic variants between BX and BM pigs. Here, the 2.56-Gb draft genome assembly for the BX pig and an N50 contig length of approximately 11.87 kb is described, and an N50 scaffold length of approximately 99 kb and the variations in the BX pig genome were identified by comparison with the BM pig reference genome. There were 1,424,354 single nucleotide polymorphisms (SNPs), 2,961,891 insertions and deletions (indels), 13,772 structural variants (SVs), and 20,606 copy number variants (CNVs) identified in the BX genome. Functional annotation of SVs and CNVs showed that the genes (ADGRE2, GPR143, olfactory receptor 52B4-like, olfactory receptor 10H1-like and SHROOM2) with both SVs and CNVs were enriched in the most of all KEGG pathways and gene ontology (GO) terms of mutant genes. ADGRE2, GPR143 and SHROOM2 were both found to have significant higher expression levels in BX pigs than in BM pigs. In the contrary, the expressions of olfactory receptor 52B4-like and olfactory receptor 10H1-like were significant lower in BX pigs than in BM pigs. In conclusion, sequence analysis of the BX pig genome revealed that the genome structure of the two pig strains has considerable genomic variation that was caused by the long inbreeding period. Moreover, qRT-PCR analysis of the mutant genes displayed a significant distinction that may be associated with phenotypic differences between these pig strains.

Keywords: Bama Xiang pig; De novo assembly; Genomics; Inbred variations.

MeSH terms

Animals
Chromosome Mapping
DNA Copy Number Variations
Gene Expression Profiling
Gene Expression Regulation
Genetic Variation*
Genome Size
High-Throughput Nucleotide Sequencing
INDEL Mutation
Inbreeding / methods*
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Swine / genetics*
Whole Genome Sequencing / methods*