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. 2009 Apr 24;324(5926):522-8.
doi: 10.1126/science.1169588.

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Bovine Genome Sequencing and Analysis ConsortiumChristine G ElsikRoss L TellamKim C WorleyRichard A GibbsDonna M MuznyGeorge M WeinstockDavid L AdelsonEvan E EichlerLaura ElnitskiRoderic GuigóDebora L HamernikSteve M KappesHarris A LewinDavid J LynnFrank W NicholasAlexandre ReymondMonique RijnkelsLoren C SkowEvgeny M ZdobnovLawrence SchookJames WomackTyler AliotoStylianos E AntonarakisAlex AstashynCharles E ChappleHsiu-Chuan ChenJacqueline ChrastFrancisco CâmaraOlga ErmolaevaCharlotte N HenrichsenWratko HlavinaYuri KapustinBoris KiryutinPaul KittsFelix KokocinskiMelissa LandrumDonna MaglottKim PruittVictor SapojnikovStephen M SearleVictor SolovyevAlexandre SouvorovCatherine UclaCarine WyssJuan M AnzolaDaniel GerlachEran ElhaikDan GraurJustin T ReeseRobert C EdgarJohn C McEwanGemma M PayneJoy M RaisonThomas JunierEvgenia V KriventsevaEduardo EyrasMireya PlassRavikiran DonthuDenis M LarkinJames ReecyMary Q YangLin ChenZe ChengCarol G Chitko-McKownGeorge E LiuLakshmi K MatukumalliJiuzhou SongBin ZhuDaniel G BradleyFiona S L BrinkmanLilian P L LauMatthew D WhitesideAngela WalkerThomas T WheelerTheresa CaseyJ Bruce GermanDanielle G LemayNauman J MaqboolAdrian J MolenaarSeongwon SeoPaul StothardCynthia L BaldwinRebecca BaxterCandice L Brinkmeyer-LangfordWendy C BrownChristopher P ChildersTimothy ConnelleyShirley A EllisKrista FritzElizabeth J GlassCarolyn T A HerzigAntti IivanainenKevin K LahmersAnna K BennettC Michael DickensJames G R GilbertDarren E HagenHanni SalihJan AertsAlexandre R CaetanoBrian DalrympleJose Fernando GarciaClare A GillStefan G HiendlederErdogan MemiliDiane SpurlockJohn L WilliamsLee AlexanderMichael J BrownsteinLeluo GuanRobert A HoltSteven J M JonesMarco A MarraRichard MooreStephen S MooreAndy RobertsMasaaki TaniguchiRichard C WatermanJoseph ChackoMimi M ChandraboseAndy CreeMarvin Diep DaoHuyen H DinhRamatu Ayiesha GabisiSandra HinesJennifer HumeShalini N JhangianiVandita JoshiChristie L KovarLora R LewisYih-Shin LiuJohn LopezMargaret B MorganNgoc Bich NguyenGeoffrey O OkwuonuSan Juana RuizJireh SantibanezRita A WrightChristian BuhayYan DingShannon Dugan-RochaJudith HerdandezMichael HolderAniko SaboAmy EganJason GoodellKatarzyna Wilczek-BoneyGerald R FowlerMatthew Edward HitchensRyan J LozadoCharles MoenDavid SteffenJames T WarrenJingkun ZhangReadman ChiuJacqueline E ScheinK James DurbinPaul HavlakHuaiyang JiangYue LiuXiang QinYanru RenYufeng ShenHenry SongStephanie Nicole BellClay DavisAngela Jolivet JohnsonSandra LeeLynne V NazarethBella Mayurkumar PatelLing-Ling PuSelina VattathilRex Lee Williams JrStacey CurryCerissa HamiltonErica SodergrenDavid A WheelerWes BarrisGary L BennettAndré EggenRonnie D GreenGregory P HarhayMatthew HobbsOliver JannJohn W KeeleMatthew P KentSigbjørn LienStephanie D McKaySean McWilliamAbhirami RatnakumarRobert D SchnabelTimothy SmithWarren M SnellingTad S SonstegardRoger T StoneYoshikazu SugimotoAkiko TakasugaJeremy F TaylorCurtis P Van TassellMichael D MacneilAntonio R R AbatepauloColette A AbbeyVirpi AholaIassudara G AlmeidaAriel F AmadioElen AnatrielloSuria M BahadueFernando H BiaseClayton R BoldtJeffery A CarrollWanessa A CarvalhoEliane P CervelattiElsa ChackoJennifer E ChapinYe ChengJungwoo ChoiAdam J ColleyTatiana A de CamposMarcos De DonatoIsabel K F de Miranda SantosCarlo J F de OliveiraHeather DeobaldEve DevinoyKaitlin E DonohuePeter DovcAnnett EberleinCarolyn J FitzsimmonsAlessandra M FranzinGustavo R GarciaSem GeniniCody J GladneyJason R GrantMarion L GreaserJonathan A GreenDarryl L HadsellHatam A HakimovRob HalgrenJennifer L HarrowElizabeth A HartNicola HastingsMarta HernandezZhi-Liang HuAaron InghamTerhi Iso-TouruCatherine JamisKirsty JensenDimos KapetisTovah KerrSari S KhalilHasan KhatibDavood KolbehdariCharu G KumarDinesh KumarRichard LeachJustin C-M LeeChangxi LiKrystin M LoganRoberto MalinverniElisa MarquesWilliam F MartinNatalia F MartinsSandra R MaruyamaRaffaele MazzaKim L McLeanJuan F MedranoBarbara T MorenoDaniela D MoréCarl T MunteanHari P NandakumarMarcelo F G NogueiraIngrid OlsakerSameer D PantFrancesca PanzittaRosemeire C P PastorMario A PoliNathan PoslusnySatyanarayana RachaganiShoba RanganathanAndrej RazpetPenny K RiggsGonzalo RinconNelida Rodriguez-OsorioSandra L Rodriguez-ZasNatasha E RomeroAnne RosenwaldLillian SandoSheila M SchmutzLibing ShenLaura ShermanBruce R SoutheyYlva Strandberg LutzowJonathan V SweedlerImke TammenBhanu Prakash V L TeluguJennifer M UrbanskiYuri T UtsunomiyaChris P VerschoorAshley J WaardenbergZhiquan WangRobert WardRosemarie WeikardThomas H Welsh JrStephen N WhiteLaurens G WilmingKris R WunderlichJianqi YangFeng-Qi Zhao
Free PMC article

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Bovine Genome Sequencing and Analysis Consortium et al. Science. .
Free PMC article

Abstract

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Figures

Fig. 1
Fig. 1
Protein orthology comparison among genomes of cattle, dog, human, mouse and rat (Bos taurus, Canis familiaris, Homo sapiens, Mus musculus, Rattus norvegicus, representing placental mammals), opossum (Monodelphis domestica; marsupial), and platypus (Ornithorhynchus anatinus; monotreme). (A) The majority of mammalian genes are orthologous, with over half preserved as single-copies (dark blue); a few thousand have species-specific duplications (blue); another few thousand have been lost in specific lineages (orange). We also show those lacking confident orthology assignment (green), and those that are apparently lineage specific [unique (white)]. Placental-specific orthologs are shown in pink. Single- or multiple-copy genes were defined on the basis of representatives in human, bovine or dog, mouse or rat, and opossum or platypus. (B) Venn diagram showing shared orthologous groups (duplicated genes were counted as one) between laurasiatherians (cattle and dog), human, rodents (mouse and rat), and non-placental mammals (opossum and platypus) on the basis of the presence of a representative gene in at least one of the grouped species (as in A). (C) Distribution of ortholog protein identities between human and the other species for a subset of strictly conserved single-copy orthologs. (D) A maximum likelihood phylogenetic tree using all single-copy orthologs supports the accepted phylogeny and quantifies the relative rates of molecular evolution expressed as the branch lengths.
Fig. 2
Fig. 2
Examples of evolutionary breakpoint regions (EBRs). Ferungulate- artiodactyl- and primate-specific EBRs on HSA1 at 175-247 Mbp (other lineage-specific EBRs not shown). Homologous synteny blocks constructed for the macaque, chimp, cattle, dog, mouse, rat and pig genomes were used for pair-wise comparisons (4). White areas correspond to EBRs. Arrows to the right of the chromosome ideogram indicate positions of representative cattle-specific, artiodactyl-specific (specific to the chromosomes of pigs and cattle), ferungulate-specific (cattle, dog and pig), primate-specific (human, macaque, chimp), and hominoid-specific (human and chimp) rearrangements. Opossum is shown as an outgroup to the eutherian clade, which allows classification of ferungulate-specific EBRs.

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