title: The sheep genome illuminates biology of the rumen and lipid metabolism.
abstract: Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.|CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.|College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Min
authors.initials: M
authors.lastname: Xie
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Chen
authors.affiliation: Ediburgh Genomics, University of Edinburgh, Easter Bush, Midlothian EH 25 9RG, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Talbot
authors.affiliation: Department of Veterinary Science, University of Melbourne, Victoria 3010, Australia.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Maddox
authors.affiliation: INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
authors.affiliation: Utah State University, Logan, UT 84322-1435-1435, USA.
authors.forename: Chunhua
authors.initials: C
authors.lastname: Wu
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.|Inner Mongolia Agricultural University, Hohhot 010018, China.|Institute of ATCG, Nei Mongol Bio-Information, Hohhot, China.
authors.forename: Wenguang
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Anatomy, University of Otago, Dunedin 9054, New Zealand.
authors.forename: Jo-Ann
authors.initials: JA
authors.lastname: Stanton
authors.affiliation: AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand.
authors.forename: Rudiger
authors.initials: R
authors.lastname: Brauning
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Barris
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
authors.forename: Thibaut
authors.initials: T
authors.lastname: Hourlier
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
authors.forename: Bronwen L
authors.initials: BL
authors.lastname: Aken
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Stephen M J
authors.initials: SMJ
authors.lastname: Searle
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: David L
authors.initials: DL
authors.lastname: Adelson
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Bian
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Graham R
authors.initials: GR
authors.lastname: Cam
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Shifeng
authors.initials: S
authors.lastname: Cheng
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Udaya
authors.initials: U
authors.lastname: DeSilva
authors.affiliation: Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark.
authors.forename: Karen
authors.initials: K
authors.lastname: Dixen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Fan
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Franklin
authors.affiliation: Inner Mongolia Agricultural University, Hohhot 010018, China.
authors.forename: Shaoyin
authors.initials: S
authors.lastname: Fu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Guan
authors.affiliation: USDA-ARS Animal Disease Research Unit, Pullman, WA 99164 USA.|Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA 99164 USA.
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Highland
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Holder
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guodong
authors.initials: G
authors.lastname: Huang
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Aaron B
authors.initials: AB
authors.lastname: Ingham
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Shalini N
authors.initials: SN
authors.lastname: Jhangiani
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Divya
authors.initials: D
authors.lastname: Kalra
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Christie L
authors.initials: CL
authors.lastname: Kovar
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Sandra L
authors.initials: SL
authors.lastname: Lee
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Weiqing
authors.initials: W
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Changxin
authors.initials: C
authors.lastname: Lu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Lv
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Tittu
authors.initials: T
authors.lastname: Mathew
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Sean
authors.initials: S
authors.lastname: McWilliam
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Moira
authors.initials: M
authors.lastname: Menzies
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Shengkai
authors.initials: S
authors.lastname: Pan
authors.affiliation: INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France.
authors.forename: David
authors.initials: D
authors.lastname: Robelin
authors.affiliation: INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Servin
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Townley
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Wenliang
authors.initials: W
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wei
authors.affiliation: USDA-ARS Animal Disease Research Unit, Pullman, WA 99164 USA.|Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA 99164 USA.
authors.forename: Stephen N
authors.initials: SN
authors.lastname: White
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Ye
authors.affiliation: Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou,730050,China.
authors.forename: Yaojing
authors.initials: Y
authors.lastname: Yue
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zeng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark.
authors.forename: Jacob B
authors.initials: JB
authors.lastname: Hansen
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristensen
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.affiliation: Biosciences KTN, The Roslin Institute, Easter Bush, Midlothian, EH25 9RG, UK.
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Warkup
authors.affiliation: Biosciences KTN, The Roslin Institute, Easter Bush, Midlothian, EH25 9RG, UK.
authors.forename: Huw E
authors.initials: HE
authors.lastname: Jones
authors.affiliation: School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
authors.forename: V Hutton
authors.initials: VH
authors.lastname: Oddy
authors.affiliation: Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia.
authors.forename: Frank W
authors.initials: FW
authors.lastname: Nicholas
authors.affiliation: AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand.
authors.forename: John C
authors.initials: JC
authors.lastname: McEwan
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: James
authors.initials: J
authors.lastname: Kijas
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.|Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.|Macau University of Science and Technology, Macau 999078, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Kim C
authors.initials: KC
authors.lastname: Worley
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH 25 9RG, UK.
authors.forename: Alan L
authors.initials: AL
authors.lastname: Archibald
authors.affiliation: Utah State University, Logan, UT 84322-1435-1435, USA.
authors.forename: Noelle
authors.initials: N
authors.lastname: Cockett
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Dalrymple
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005232:Fatty Acids, Volatile / Q000378:metabolism / Q000502:physiology; D005786:Gene Expression Regulation; D016678:Genome; D053564:Keratins, Hair-Specific / Q000235:genetics; D050356:Lipid Metabolism / Q000235:genetics / Q000502:physiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012417:Rumen / Q000378:metabolism / Q000502:physiology*; D034561:Sheep, Domestic / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D059467:Transcriptome; D014935:Wool / Q000254:growth & development
chemical_list: D005232:Fatty Acids, Volatile; D053564:Keratins, Hair-Specific