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PMID: 16341006 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Nature ·Vol. 438 ·No. 7069 ·2005-12-08 ·Pages 803-19

Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, 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 SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES

Abstract

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

MeSH Terms
Animals Conserved Sequence/genetics Dog Diseases/genetics Dogs/classification,genetics Evolution, Molecular Female Genome/genetics Genomics Haplotypes/genetics Humans Hybridization, Genetic Male Mice Mutagenesis/genetics Polymorphism, Single Nucleotide/genetics Rats Short Interspersed Nucleotide Elements/genetics Synteny/genetics
Authors & Affiliations
236 authors, click to expand affiliations / ORCID
Lindblad-Toh Kerstin
Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA. kersli@broad.mit.edu
Wade Claire M
Mikkelsen Tarjei S
Karlsson Elinor K
Jaffe David B
Kamal Michael
Clamp Michele
Chang Jean L
Kulbokas Edward J
Zody Michael C
Mauceli Evan
Xie Xiaohui
Breen Matthew
Wayne Robert K
Ostrander Elaine A
Ponting Chris P
Galibert Francis
Smith Douglas R
DeJong Pieter J
Kirkness Ewen
Alvarez Pablo
Biagi Tara
Brockman William
Butler Jonathan
Chin Chee-Wye
Cook April
Cuff James
Daly Mark J
DeCaprio David
Gnerre Sante
Grabherr Manfred
Kellis Manolis
Kleber Michael
Bardeleben Carolyne
Goodstadt Leo
Heger Andreas
Hitte Christophe
Kim Lisa
Koepfli Klaus-Peter
Parker Heidi G
Pollinger John P
Searle Stephen M J
Sutter Nathan B
Thomas Rachael
Webber Caleb
Baldwin Jennifer
Abebe Adal
Abouelleil Amr
Aftuck Lynne
Ait-Zahra Mostafa
Aldredge Tyler
Allen Nicole
An Peter
Anderson Scott
Antoine Claudel
Arachchi Harindra
Aslam Ali
Ayotte Laura
Bachantsang Pasang
Barry Andrew
Bayul Tashi
Benamara Mostafa
Berlin Aaron
Bessette Daniel
Blitshteyn Berta
Bloom Toby
Blye Jason
Boguslavskiy Leonid
Bonnet Claude
Boukhgalter Boris
Brown Adam
Cahill Patrick
Calixte Nadia
Camarata Jody
Cheshatsang Yama
Chu Jeffrey
Citroen Mieke
Collymore Alville
Cooke Patrick
Dawoe Tenzin
Daza Riza
Decktor Karin
DeGray Stuart
Dhargay Norbu
Dooley Kimberly
Dooley Kathleen
Dorje Passang
Dorjee Kunsang
Dorris Lester
Duffey Noah
Dupes Alan
Egbiremolen Osebhajajeme
Elong Richard
Falk Jill
Farina Abderrahim
Faro Susan
Ferguson Diallo
Ferreira Patricia
Fisher Sheila
FitzGerald Mike
Foley Karen
Foley Chelsea
Franke Alicia
Friedrich Dennis
Gage Diane
Garber Manuel
Gearin Gary
Giannoukos Georgia
Goode Tina
Goyette Audra
Graham Joseph
Grandbois Edward
Gyaltsen Kunsang
Hafez Nabil
Hagopian Daniel
Hagos Birhane
Hall Jennifer
Healy Claire
Hegarty Ryan
Honan Tracey
Horn Andrea
Houde Nathan
Hughes Leanne
Hunnicutt Leigh
Husby M
Jester Benjamin
Jones Charlien
Kamat Asha
Kanga Ben
Kells Cristyn
Khazanovich Dmitry
Kieu Alix Chinh
Kisner Peter
Kumar Mayank
Lance Krista
Landers Thomas
Lara Marcia
Lee William
Leger Jean-Pierre
Lennon Niall
Leuper Lisa
LeVine Sarah
Liu Jinlei
Liu Xiaohong
Lokyitsang Yeshi
Lokyitsang Tashi
Lui Annie
Macdonald Jan
Major John
Marabella Richard
Maru Kebede
Matthews Charles
McDonough Susan
Mehta Teena
Meldrim James
Melnikov Alexandre
Meneus Louis
Mihalev Atanas
Mihova Tanya
Miller Karen
Mittelman Rachel
Mlenga Valentine
Mulrain Leonidas
Munson Glen
Navidi Adam
Naylor Jerome
Nguyen Tuyen
Nguyen Nga
Nguyen Cindy
Nguyen Thu
Nicol Robert
Norbu Nyima
Norbu Choe
Novod Nathaniel
Nyima Tenchoe
Olandt Peter
O'Neill Barry
O'Neill Keith
Osman Sahal
Oyono Lucien
Patti Christopher
Perrin Danielle
Phunkhang Pema
Pierre Fritz
Priest Margaret
Rachupka Anthony
Raghuraman Sujaa
Rameau Rayale
Ray Verneda
Raymond Christina
Rege Filip
Rise Cecil
Rogers Julie
Rogov Peter
Sahalie Julie
Settipalli Sampath
Sharpe Theodore
Shea Terrance
Sheehan Mechele
Sherpa Ngawang
Shi Jianying
Shih Diana
Sloan Jessie
Smith Cherylyn
Sparrow Todd
Stalker John
Stange-Thomann Nicole
Stavropoulos Sharon
Stone Catherine
Stone Sabrina
Sykes Sean
Tchuinga Pierre
Tenzing Pema
Tesfaye Senait
Thoulutsang Dawa
Thoulutsang Yama
Topham Kerri
Topping Ira
Tsamla Tsamla
Vassiliev Helen
Venkataraman Vijay
Vo Andy
Wangchuk Tsering
Wangdi Tsering
Weiand Michael
Wilkinson Jane
Wilson Adam
Yadav Shailendra
Yang Shuli
Yang Xiaoping
Young Geneva
Yu Qing
Zainoun Joanne
Zembek Lisa
Zimmer Andrew
Lander Eric S
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
Published
2005-12-08
Pages
803-19
Language
English
Region
England
NLM ID
0410462
Subset
IM
Grants
Intramural NIH HHS · United States
Corrections
CommentIn
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