title: Global copy number analyses by next generation sequencing provide insight into pig genome variation.
abstract: BACKGROUND
  Copy number variations (CNVs) confer significant effects on genetic innovation and phenotypic variation. Previous CNV studies in swine seldom focused on in-depth characterization of global CNVs.
  
  
  RESULTS
  Using whole-genome assembly comparison (WGAC) and whole-genome shotgun sequence detection (WSSD) approaches by next generation sequencing (NGS), we probed formation signatures of both segmental duplications (SDs) and individualized CNVs in an integrated fashion, building the finest resolution CNV and SD maps of pigs so far. We obtained copy number estimates of all protein-coding genes with copy number variation carried by individuals, and further confirmed two genes with high copy numbers in Meishan pigs through an enlarged population. We determined genome-wide CNV hotspots, which were significantly enriched in SD regions, suggesting evolution of CNV hotspots may be affected by ancestral SDs. Through systematically enrichment analyses based on simulations and bioinformatics analyses, we revealed CNV-related genes undergo a different selective constraint from those CNV-unrelated regions, and CNVs may be associated with or affect pig health and production performance under recent selection.
  
  
  CONCLUSIONS
  Our studies lay out one way for characterization of CNVs in the pig genome, provide insight into the pig genome variation and prompt CNV mechanisms studies when using pigs as biomedical models for human diseases.
authors.forename: Jicai
authors.initials: J
authors.lastname: Jiang
authors.forename: Jiying
authors.initials: J
authors.lastname: Wang
authors.forename: Haifei
authors.initials: H
authors.lastname: Wang
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Huimin
authors.initials: H
authors.lastname: Kang
authors.forename: Xiaotian
authors.initials: X
authors.lastname: Feng
authors.forename: Jiafu
authors.initials: J
authors.lastname: Wang
authors.forename: Zongjun
authors.initials: Z
authors.lastname: Yin
authors.forename: Wenbin
authors.initials: W
authors.lastname: Bao
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. liujf@cau.edu.cn.
authors.forename: Jian-Feng
authors.initials: JF
authors.lastname: Liu
mesh_terms: D000818:Animals; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D018628:Gene Dosage; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics*