Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

被引：575

作者：

Wade, C. M. ^{[1
,2
,3
]}

Giulotto, E. ^{[4
]}

Sigurdsson, S. ^{[1
,5
]}

Zoli, M. ^{[6
]}

Gnerre, S. ^{[1
]}

Imsland, F. ^{[5
]}

Lear, T. L. ^{[7
]}

Adelson, D. L. ^{[8
]}

Bailey, E. ^{[7
]}

Bellone, R. R. ^{[9
]}

Bloecker, H. ^{[10
]}

Distl, O. ^{[11
]}

Edgar, R. C.

Garber, M. ^{[1
]}

Leeb, T. ^{[11
,12
]}

Mauceli, E. ^{[1
]}

MacLeod, J. N. ^{[7
]}

Penedo, M. C. T. ^{[13
]}

Raison, J. M. ^{[8
]}

Sharpe, T. ^{[1
]}

Vogel, J. ^{[14
]}

Andersson, L. ^{[5
]}

Antczak, D. F. ^{[15
]}

Biagi, T. ^{[1
]}

Binns, M. M. ^{[16
]}

Chowdhary, B. P. ^{[8
]}

Coleman, S. J. ^{[7
]}

Della Valle, G. ^{[6
]}

Fryc, S. ^{[1
]}

Guerin, G. ^{[18
]}

Hasegawa, T. ^{[19
]}

Hill, E. W. ^{[20
]}

Jurka, J. ^{[21
]}

Kiialainen, A. ^{[22
]}

Lindgren, G. ^{[23
]}

Liu, J. ^{[24
]}

Magnani, E. ^{[4
]}

Mickelson, J. R. ^{[25
]}

Murray, J. ^{[26
]}

Nergadze, S. G. ^{[4
]}

Onofrio, R. ^{[1
]}

Pedroni, S. ^{[13
]}

Piras, M. F. ^{[4
]}

Raudsepp, T. ^{[8
]}

Rocchi, M. ^{[27
]}

Roed, K. H. ^{[9
]}

Ryder, O. A. ^{[28
]}

Searle, S. ^{[14
]}

Skow, L. ^{[17
]}

Swinburne, J. E. ^{[29
]}

机构：

[1] Broad Inst, Cambridge, MA 02142 USA

[2] Massachusetts Gen Hosp, Ctr Human Genet Res, Boston, MA 02114 USA

[3] Univ Sydney, Fac Vet Sci, Sydney, NSW 2006, Australia

[4] Univ Pavia, Dipartimento Genet & Microbiol, I-27100 Pavia, Italy

[5] Uppsala Univ, Dept Med Biochem & Microbiol, SE-75124 Uppsala, Sweden

[6] Univ Bologna, Dipartimento Biol, I-40126 Bologna, Italy

[7] Univ Kentucky, Dept Vet Sci, Maxwell H Gluck Equine Res Ctr, Lexington, KY 40546 USA

[8] Univ Adelaide, Adelaide, SA 5005, Australia

[9] Univ Tampa, Tampa, FL 33606 USA

[10] Helmholtz Ctr Infect Res, Braunschweig, Germany

[11] Univ Vet Med Hannover, Inst Genet & Anim Breeding, D-30559 Hannover, Germany

[12] Univ Bern, Vetsuisse Fac, Inst Genet, CH-3001 Bern, Switzerland

[13] Univ Calif Davis, Vet Genet Lab, Davis, CA 95616 USA

[14] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[15] Cornell Univ, Coll Vet Med, James A Baker Inst Anim Hlth, Ithaca, NY 14853 USA

[16] Univ London Royal Vet Coll, London NW1 0TU, England

[17] Texas A&M Univ, Coll Vet Med, College Stn, TX 77843 USA

[18] INRA, UMR 1313, F-44078350 Jouy En Josas, France

[19] Japan Racing Assoc, Equine Res Inst, Utsunomiya, Tochigi 3200856, Japan

[20] Univ Coll Dublin, Sch Agr Food Sci & Vet Med, Anim Genom Lab, Dublin 4, Ireland

[21] Genet Informat Res Inst, Mountain View, CA 94043 USA

[22] Uppsala Univ, Dept Med Sci, S-75185 Uppsala, Sweden

[23] Swedish Univ Agr Sci, Dept Anim Breeding & Genet, SE-75124 Uppsala, Sweden

[24] Univ Kentucky, Dept Comp Sci, Lexington, KY 40506 USA

[25] Univ Minnesota, Coll Vet Med, St Paul, MN 55108 USA

[26] Univ Calif Davis, Sch Vet Med, Davis, CA 95616 USA

[27] Univ Bari, Dept Genet & Microbiol, I-70126 Bari, Italy

[28] San Diego Zoos Inst Conservat Res, Escondido, CA 92029 USA

[29] Anim Hlth Trust, Newmarket CB8 7UU, Suffolk, England

[30] Lab Racing Chem, Dept Mol Genet, Utsunomiya, Tochigi 3200851, Japan

[31] MIT, Dept Biol, Cambridge, MA 02142 USA

来源：

SCIENCE | 2009年 / 326卷 / 5954期

基金：

美国国家科学基金会;

关键词：

STATIONARY NIGHT BLINDNESS; CENTROMERES; APPALOOSA; EVOLUTION; CATTLE;

D O I：

10.1126/science.1178158

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

We report a high-quality draft sequence of the genome of the horse ( Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

引用

页码：865 / 867

页数：3

共 17 条

[1] Differential gene expression of TPLPM1, the potential cause of congenital stationary night blindness and coat spotting patterns (LP) in the appaloosa horse (Equus caballus) [J].

Bellone, Rebecca R. ;

Brooks, Samantha A. ;

Sandmeyer, Lynne ;

Murphy, Barbara A. ;

Forsyth, George ;

Archer, Sheila ;

Bailey, Ernest ;

Grahn, Bruce .

GENETICS, 2008, 179 (04) :1861-1870

[2] Evolutionary movement of centromeres in horse, donkey, and zebra [J].

Carbone, Lucia ;

Nergadze, Solomon G. ;

Magnani, Elisa ;

Misceo, Doriana ;

Cardone, Maria Francesca ;

Roberto, Roberta ;

Bertoni, Livia ;

Attolini, Carmen ;

Piras, Maria Francesca ;

de Jong, Pieter ;

Raudsepp, Terje ;

Chowdhary, Bhanu P. ;

Guerin, Gerard ;

Archidiacono, Nicoletta ;

Rocchi, Mariano ;

Giulotto, Elena .

GENOMICS, 2006, 87 (06) :777-782

[3] A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres [J].

Carone, Dawn M. ;

Longo, Mark S. ;

Ferreri, Gianni C. ;

Hall, Laura ;

Harris, Melissa ;

Shook, Nicole ;

Bulazel, Kira V. ;

Carone, Benjamin R. ;

Obergfell, Craig ;

O'Neill, Michael J. ;

O'Neill, Rachel J. .

CHROMOSOMA, 2009, 118 (01) :113-125

[4] Potential applications of equine genomics in dissecting diseases and fertility [J].

Chowdhary, Bhanu P. ;

Paria, Nandina ;

Raudsepp, Terje .

ANIMAL REPRODUCTION SCIENCE, 2008, 107 (3-4) :208-218

[5] LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin [J].

Chueh, Anderly C. ;

Northrop, Emma L. ;

Brettingham-Moore, Kate H. ;

Choo, K. H. Andy ;

Wong, Lee H. .

PLOS GENETICS, 2009, 5 (01)

[6] The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution [J].

Elsik, Christine G. ;

Tellam, Ross L. ;

Worley, Kim C. ;

Gibbs, Richard A. ;

Abatepaulo, Antonio R. R. ;

Abbey, Colette A. ;

Adelson, David L. ;

Aerts, Jan ;

Ahola, Virpi ;

Alexander, Lee ;

Alioto, Tyler ;

Almeida, Iassudara G. ;

Amadio, Ariel F. ;

Anatriello, Elen ;

Antonarakis, Stylianos E. ;

Anzola, Juan M. ;

Astashyn, Alex ;

Bahadue, Suria M. ;

Baldwin, Cynthia L. ;

Barris, Wes ;

Baxter, Rebecca ;

Bell, Stephanie Nicole ;

Bennett, Anna K. ;

Bennett, Gary L. ;

Biase, Fernando H. ;

Boldt, Clayton R. ;

Bradley, Daniel G. ;

Brinkman, Fiona S. L. ;

Brinkmeyer-Langford, Candice L. ;

Brown, Wendy C. ;

Brownstein, Michael J. ;

Buhay, Christian ;

Caetano, Alexandre R. ;

Camara, Francisco ;

Carroll, Jeffrey A. ;

Carvalho, Wanessa A. ;

Casey, Theresa ;

Cervelatti, Elaine P. ;

Chack, Joseph ;

Chacko, Elsa ;

Chandrabose, Mimi M. ;

Chapin, Jennifer E. ;

Chapple, Charles E. ;

Chen, Hsiu-Chuan ;

Chen, Lin ;

Cheng, Ye ;

Cheng, Ze ;

Childers, Christopher P. ;

Chitko-McKown, Carol G. ;

Chiu, Readman .

SCIENCE, 2009, 324 (5926) :522-528

[7] Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds [J].

Gibbs, Richard A. ;

Taylor, Jeremy F. ;

Van Tassell, Curtis P. ;

Barendse, William ;

Eversoie, Kallye A. ;

Gill, Clare A. ;

Green, Ronnie D. ;

Hamernik, Debora L. ;

Kappes, Steven M. ;

Lien, Sigbjorn ;

Matukumalli, Lakshmi K. ;

McEwan, John C. ;

Nazareth, Lynne V. ;

Schnabel, Robert D. ;

Taylor, Jeremy F. ;

Weinstock, George M. ;

Wheeler, David A. ;

Ajmone-Marsan, Paolo ;

Barendse, William ;

Boettcher, Paul J. ;

Caetano, Alexandre R. ;

Garcia, Jose Fernando ;

Hanotte, Olivier ;

Mariani, Paola ;

Skow, Loren C. ;

Williams, John L. ;

Caetano, Alexandre R. ;

Diallo, Boubacar ;

Green, Ronnie D. ;

Hailemariam, Lemecha ;

Hanotte, Olivier ;

Martinez, Mario L. ;

Morris, Chris A. ;

Silva, Luiz O. C. ;

Spelman, Richard J. ;

Taylor, Jeremy F. ;

Mulatu, Woudyalew ;

Zhao, Keyan ;

Abbey, Colette A. ;

Agaba, Morris ;

Araujo, Flabio R. ;

Bunch, Rowan J. ;

Burton, James ;

Gill, Clare A. ;

Gorni, Chiara ;

Olivier, Hanotte ;

Harrison, Blair E. ;

Luff, Bill ;

Machado, Marco A. ;

Mariani, Paola .

SCIENCE, 2009, 324 (5926) :528-532

[8] Initial sequencing and analysis of the human genome [J].

Lander, ES ;

Int Human Genome Sequencing Consortium ;

Linton, LM ;

Birren, B ;

Nusbaum, C ;

Zody, MC ;

Baldwin, J ;

Devon, K ;

Dewar, K ;

Doyle, M ;

FitzHugh, W ;

Funke, R ;

Gage, D ;

Harris, K ;

Heaford, A ;

Howland, J ;

Kann, L ;

Lehoczky, J ;

LeVine, R ;

McEwan, P ;

McKernan, K ;

Meldrim, J ;

Mesirov, JP ;

Miranda, C ;

Morris, W ;

Naylor, J ;

Raymond, C ;

Rosetti, M ;

Santos, R ;

Sheridan, A ;

Sougnez, C ;

Stange-Thomann, N ;

Stojanovic, N ;

Subramanian, A ;

Wyman, D ;

Rogers, J ;

Sulston, J ;

Ainscough, R ;

Beck, S ;

Bentley, D ;

Burton, J ;

Clee, C ;

Carter, N ;

Coulson, A ;

Deadman, R ;

Deloukas, P ;

Dunham, A ;

Dunham, I ;

Durbin, R ;

French, L .

NATURE, 2001, 409 (6822) :860-921

[9] Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences [J].

Lau, Allison N. ;

Peng, Lei ;

Goto, Hiroki ;

Chemnick, Leona ;

Ryder, Oliver A. ;

Makova, Kateryna D. .

MOLECULAR BIOLOGY AND EVOLUTION, 2009, 26 (01) :199-208

[10] Genome sequence, comparative analysis and haplotype structure of the domestic dog [J].

Lindblad-Toh, K ;

Wade, CM ;

Mikkelsen, TS ;

Karlsson, EK ;

Jaffe, DB ;

Kamal, M ;

Clamp, M ;

Chang, JL ;

Kulbokas, EJ ;

Zody, MC ;

Mauceli, E ;

Xie, XH ;

Breen, M ;

Wayne, RK ;

Ostrander, EA ;

Ponting, CP ;

Galibert, F ;

Smith, DR ;

deJong, PJ ;

Kirkness, E ;

Alvarez, P ;

Biagi, T ;

Brockman, W ;

Butler, J ;

Chin, CW ;

Cook, A ;

Cuff, J ;

Daly, MJ ;

DeCaprio, D ;

Gnerre, S ;

Grabherr, M ;

Kellis, M ;

Kleber, M ;

Bardeleben, C ;

Goodstadt, L ;

Heger, A ;

Hitte, C ;

Kim, L ;

Koepfli, KP ;

Parker, HG ;

Pollinger, JP ;

Searle, SMJ ;

Sutter, NB ;

Thomas, R ;

Webber, C ;

Lander, ES .

NATURE, 2005, 438 (7069) :803-819

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