Global copy number analyses by next generation sequencing provide insight into pig genome variation

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• 作者：Jicai Jiang (11)
  Jiying Wang (12)
  Haifei Wang (11)
  Yan Zhang (13)
  Huimin Kang (11)
  Xiaotian Feng (11)
  Jiafu Wang (14)
  Zongjun Yin (15)
  Wenbin Bao (16)
  Qin Zhang (11)
  Jian-Feng Liu (11)
  
  11. 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
  12. Shandong Provincial Key Laboratory of Animal Disease Control and Breeding ; Institute of Animal Science and Veterinary Medicine ; Shandong Academy of Agricultural Sciences ; Jinan ; 250100 ; China
  13. Virginia Bioinformatics Institute ; Virginia Tech ; Washington Street ; Blacksburg ; Virginia ; MC0477 ; 24061 ; USA
  14. School of Animal Science ; Guizhou University ; Guiyang ; 550025 ; China
  15. College of Animal Science and Technology ; Anhui Agricultural University ; Hefei ; 230036 ; China
  16. College of Animal Science and Technology ; Yangzhou University ; Yangzhou ; 225009 ; China
  
• 关键词：Copy number variations (CNVs) ; Segmental duplications (SDs) ; Next generation sequencing (NGS) ; Pigs
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,369 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

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.