Genome sequence, comparative analysis and haplotype structure of the domestic dog.
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.
Lindblad-Toh
Kerstin
K
Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA. kersli@broad.mit.edu
Wade
Claire M
CM
Mikkelsen
Tarjei S
TS
Karlsson
Elinor K
EK
Jaffe
David B
DB
Kamal
Michael
M
Clamp
Michele
M
Chang
Jean L
JL
Kulbokas
Edward J
EJ
Zody
Michael C
MC
Mauceli
Evan
E
Xie
Xiaohui
X
Breen
Matthew
M
Wayne
Robert K
RK
Ostrander
Elaine A
EA
Ponting
Chris P
CP
Galibert
Francis
F
Smith
Douglas R
DR
DeJong
Pieter J
PJ
Kirkness
Ewen
E
Alvarez
Pablo
P
Biagi
Tara
T
Brockman
William
W
Butler
Jonathan
J
Chin
Chee-Wye
CW
Cook
April
A
Cuff
James
J
Daly
Mark J
MJ
DeCaprio
David
D
Gnerre
Sante
S
Grabherr
Manfred
M
Kellis
Manolis
M
Kleber
Michael
M
Bardeleben
Carolyne
C
Goodstadt
Leo
L
Heger
Andreas
A
Hitte
Christophe
C
Kim
Lisa
L
Koepfli
Klaus-Peter
KP
Parker
Heidi G
HG
Pollinger
John P
JP
Searle
Stephen M J
SM
Sutter
Nathan B
NB
Thomas
Rachael
R
Webber
Caleb
C
Baldwin
Jennifer
J
Abebe
Adal
A
Abouelleil
Amr
A
Aftuck
Lynne
L
Ait-Zahra
Mostafa
M
Aldredge
Tyler
T
Allen
Nicole
N
An
Peter
P
Anderson
Scott
S
Antoine
Claudel
C
Arachchi
Harindra
H
Aslam
Ali
A
Ayotte
Laura
L
Bachantsang
Pasang
P
Barry
Andrew
A
Bayul
Tashi
T
Benamara
Mostafa
M
Berlin
Aaron
A
Bessette
Daniel
D
Blitshteyn
Berta
B
Bloom
Toby
T
Blye
Jason
J
Boguslavskiy
Leonid
L
Bonnet
Claude
C
Boukhgalter
Boris
B
Brown
Adam
A
Cahill
Patrick
P
Calixte
Nadia
N
Camarata
Jody
J
Cheshatsang
Yama
Y
Chu
Jeffrey
J
Citroen
Mieke
M
Collymore
Alville
A
Cooke
Patrick
P
Dawoe
Tenzin
T
Daza
Riza
R
Decktor
Karin
K
DeGray
Stuart
S
Dhargay
Norbu
N
Dooley
Kimberly
K
Dooley
Kathleen
K
Dorje
Passang
P
Dorjee
Kunsang
K
Dorris
Lester
L
Duffey
Noah
N
Dupes
Alan
A
Egbiremolen
Osebhajajeme
O
Elong
Richard
R
Falk
Jill
J
Farina
Abderrahim
A
Faro
Susan
S
Ferguson
Diallo
D
Ferreira
Patricia
P
Fisher
Sheila
S
FitzGerald
Mike
M
Foley
Karen
K
Foley
Chelsea
C
Franke
Alicia
A
Friedrich
Dennis
D
Gage
Diane
D
Garber
Manuel
M
Gearin
Gary
G
Giannoukos
Georgia
G
Goode
Tina
T
Goyette
Audra
A
Graham
Joseph
J
Grandbois
Edward
E
Gyaltsen
Kunsang
K
Hafez
Nabil
N
Hagopian
Daniel
D
Hagos
Birhane
B
Hall
Jennifer
J
Healy
Claire
C
Hegarty
Ryan
R
Honan
Tracey
T
Horn
Andrea
A
Houde
Nathan
N
Hughes
Leanne
L
Hunnicutt
Leigh
L
Husby
M
M
Jester
Benjamin
B
Jones
Charlien
C
Kamat
Asha
A
Kanga
Ben
B
Kells
Cristyn
C
Khazanovich
Dmitry
D
Kieu
Alix Chinh
AC
Kisner
Peter
P
Kumar
Mayank
M
Lance
Krista
K
Landers
Thomas
T
Lara
Marcia
M
Lee
William
W
Leger
Jean-Pierre
JP
Lennon
Niall
N
Leuper
Lisa
L
LeVine
Sarah
S
Liu
Jinlei
J
Liu
Xiaohong
X
Lokyitsang
Yeshi
Y
Lokyitsang
Tashi
T
Lui
Annie
A
Macdonald
Jan
J
Major
John
J
Marabella
Richard
R
Maru
Kebede
K
Matthews
Charles
C
McDonough
Susan
S
Mehta
Teena
T
Meldrim
James
J
Melnikov
Alexandre
A
Meneus
Louis
L
Mihalev
Atanas
A
Mihova
Tanya
T
Miller
Karen
K
Mittelman
Rachel
R
Mlenga
Valentine
V
Mulrain
Leonidas
L
Munson
Glen
G
Navidi
Adam
A
Naylor
Jerome
J
Nguyen
Tuyen
T
Nguyen
Nga
N
Nguyen
Cindy
C
Nguyen
Thu
T
Nicol
Robert
R
Norbu
Nyima
N
Norbu
Choe
C
Novod
Nathaniel
N
Nyima
Tenchoe
T
Olandt
Peter
P
O'Neill
Barry
B
O'Neill
Keith
K
Osman
Sahal
S
Oyono
Lucien
L
Patti
Christopher
C
Perrin
Danielle
D
Phunkhang
Pema
P
Pierre
Fritz
F
Priest
Margaret
M
Rachupka
Anthony
A
Raghuraman
Sujaa
S
Rameau
Rayale
R
Ray
Verneda
V
Raymond
Christina
C
Rege
Filip
F
Rise
Cecil
C
Rogers
Julie
J
Rogov
Peter
P
Sahalie
Julie
J
Settipalli
Sampath
S
Sharpe
Theodore
T
Shea
Terrance
T
Sheehan
Mechele
M
Sherpa
Ngawang
N
Shi
Jianying
J
Shih
Diana
D
Sloan
Jessie
J
Smith
Cherylyn
C
Sparrow
Todd
T
Stalker
John
J
Stange-Thomann
Nicole
N
Stavropoulos
Sharon
S
Stone
Catherine
C
Stone
Sabrina
S
Sykes
Sean
S
Tchuinga
Pierre
P
Tenzing
Pema
P
Tesfaye
Senait
S
Thoulutsang
Dawa
D
Thoulutsang
Yama
Y
Topham
Kerri
K
Topping
Ira
I
Tsamla
Tsamla
T
Vassiliev
Helen
H
Venkataraman
Vijay
V
Vo
Andy
A
Wangchuk
Tsering
T
Wangdi
Tsering
T
Weiand
Michael
M
Wilkinson
Jane
J
Wilson
Adam
A
Yadav
Shailendra
S
Yang
Shuli
S
Yang
Xiaoping
X
Young
Geneva
G
Yu
Qing
Q
Zainoun
Joanne
J
Zembek
Lisa
L
Zimmer
Andrew
A
Lander
Eric S
ES
D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D004283:Dog Diseases / Q000235:genetics; D004285:Dogs / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D016678:Genome / Q000235:genetics*; D023281:Genomics; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D006824:Hybridization, Genetic; D008297:Male; D051379:Mice; D016296:Mutagenesis / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D051381:Rats; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics; D026801:Synteny / Q000235:genetics