title: Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.
abstract: BACKGROUND
  Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.
  
  
  RESULTS
  We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.
  
  
  CONCLUSIONS
  Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.
authors.affiliation: Kunming University of Science and Technology, Kunming, 650093, China. loyalyang@gmail.com.|CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. loyalyang@gmail.com.
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. xlviolet@gmail.com.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. feixue1039@gmail.com.
authors.forename: Min
authors.initials: M
authors.lastname: Xie
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Karaj, Iran. babaref@yahoo.com.
authors.forename: Babak
authors.initials: B
authors.lastname: Arefnezhad
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. wangzongji@genomics.cn.|School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China. wangzongji@genomics.cn.
authors.forename: Zongji
authors.initials: Z
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. wangwenliang@genomics.cn.
authors.forename: Wenliang
authors.initials: W
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. fengshaohong@genomics.cn.
authors.forename: Shaohong
authors.initials: S
authors.lastname: Feng
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. huangguodong@genomics.cn.
authors.forename: Guodong
authors.initials: G
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. guanrui@genomics.cn.
authors.forename: Rui
authors.initials: R
authors.lastname: Guan
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. changchangfandiao@126.com.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Shen
authors.affiliation: CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia. Rowan.Bunch@csiro.au.
authors.forename: Rowan
authors.initials: R
authors.lastname: Bunch
authors.affiliation: CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia. Russell.Mcculloch@csiro.au.
authors.forename: Russell
authors.initials: R
authors.lastname: McCulloch
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. liqiye@genomics.cn.|Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. liqiye@genomics.cn.
authors.forename: Qiye
authors.initials: Q
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. liqiye@genomics.cn.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. zhanggjconi@gmail.com.|Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. zhanggjconi@gmail.com.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. xuxun@genomics.cn.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia. James.Kijas@csiro.au.
authors.forename: James W
authors.initials: JW
authors.lastname: Kijas
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Karaj, Iran. hsalekdeh@yahoo.com.|Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran. hsalekdeh@yahoo.com.
authors.forename: Ghasem Hosseini
authors.initials: GH
authors.lastname: Salekdeh
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. wwang@mail.kiz.ac.cn.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China. jiangyu96@163.com.|College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China. jiangyu96@163.com.
authors.forename: Yu
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D000835:Animals, Wild / Q000235:genetics; D005075:Biological Evolution; D001947:Breeding; D004247:DNA / Q000032:analysis / Q000302:isolation & purification; D056915:DNA Copy Number Variations; D014644:Genetic Variation; D016678:Genome; D006041:Goats / Q000235:genetics*; D007107:Immune System / Q000378:metabolism; D008297:Male; D008969:Molecular Sequence Data; D062806:Myelin and Lymphocyte-Associated Proteolipid Proteins / Q000145:classification / Q000235:genetics; D009420:Nervous System / Q000378:metabolism; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D043886:Receptor, Cholecystokinin A / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D062806:Myelin and Lymphocyte-Associated Proteolipid Proteins; D043886:Receptor, Cholecystokinin A; D004247:DNA