Initial sequencing and comparative analysis of the mouse genome.
The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. waterston@gs.washington.edu
Waterston
Robert H
RH
Lindblad-Toh
Kerstin
K
Birney
Ewan
E
Rogers
Jane
J
Abril
Josep F
JF
Agarwal
Pankaj
P
Agarwala
Richa
R
Ainscough
Rachel
R
Alexandersson
Marina
M
An
Peter
P
Antonarakis
Stylianos E
SE
Attwood
John
J
Baertsch
Robert
R
Bailey
Jonathon
J
Barlow
Karen
K
Beck
Stephan
S
Berry
Eric
E
Birren
Bruce
B
Bloom
Toby
T
Bork
Peer
P
Botcherby
Marc
M
Bray
Nicolas
N
Brent
Michael R
MR
Brown
Daniel G
DG
Brown
Stephen D
SD
Bult
Carol
C
Burton
John
J
Butler
Jonathan
J
Campbell
Robert D
RD
Carninci
Piero
P
Cawley
Simon
S
Chiaromonte
Francesca
F
Chinwalla
Asif T
AT
Church
Deanna M
DM
Clamp
Michele
M
Clee
Christopher
C
Collins
Francis S
FS
Cook
Lisa L
LL
Copley
Richard R
RR
Coulson
Alan
A
Couronne
Olivier
O
Cuff
James
J
Curwen
Val
V
Cutts
Tim
T
Daly
Mark
M
David
Robert
R
Davies
Joy
J
Delehaunty
Kimberly D
KD
Deri
Justin
J
Dermitzakis
Emmanouil T
ET
Dewey
Colin
C
Dickens
Nicholas J
NJ
Diekhans
Mark
M
Dodge
Sheila
S
Dubchak
Inna
I
Dunn
Diane M
DM
Eddy
Sean R
SR
Elnitski
Laura
L
Emes
Richard D
RD
Eswara
Pallavi
P
Eyras
Eduardo
E
Felsenfeld
Adam
A
Fewell
Ginger A
GA
Flicek
Paul
P
Foley
Karen
K
Frankel
Wayne N
WN
Fulton
Lucinda A
LA
Fulton
Robert S
RS
Furey
Terrence S
TS
Gage
Diane
D
Gibbs
Richard A
RA
Glusman
Gustavo
G
Gnerre
Sante
S
Goldman
Nick
N
Goodstadt
Leo
L
Grafham
Darren
D
Graves
Tina A
TA
Green
Eric D
ED
Gregory
Simon
S
Guigó
Roderic
R
Guyer
Mark
M
Hardison
Ross C
RC
Haussler
David
D
Hayashizaki
Yoshihide
Y
Hillier
LaDeana W
LW
Hinrichs
Angela
A
Hlavina
Wratko
W
Holzer
Timothy
T
Hsu
Fan
F
Hua
Axin
A
Hubbard
Tim
T
Hunt
Adrienne
A
Jackson
Ian
I
Jaffe
David B
DB
Johnson
L Steven
LS
Jones
Matthew
M
Jones
Thomas A
TA
Joy
Ann
A
Kamal
Michael
M
Karlsson
Elinor K
EK
Karolchik
Donna
D
Kasprzyk
Arkadiusz
A
Kawai
Jun
J
Keibler
Evan
E
Kells
Cristyn
C
Kent
W James
WJ
Kirby
Andrew
A
Kolbe
Diana L
DL
Korf
Ian
I
Kucherlapati
Raju S
RS
Kulbokas
Edward J
EJ
Kulp
David
D
Landers
Tom
T
Leger
J P
JP
Leonard
Steven
S
Letunic
Ivica
I
Levine
Rosie
R
Li
Jia
J
Li
Ming
M
Lloyd
Christine
C
Lucas
Susan
S
Ma
Bin
B
Maglott
Donna R
DR
Mardis
Elaine R
ER
Matthews
Lucy
L
Mauceli
Evan
E
Mayer
John H
JH
McCarthy
Megan
M
McCombie
W Richard
WR
McLaren
Stuart
S
McLay
Kirsten
K
McPherson
John D
JD
Meldrim
Jim
J
Meredith
Beverley
B
Mesirov
Jill P
JP
Miller
Webb
W
Miner
Tracie L
TL
Mongin
Emmanuel
E
Montgomery
Kate T
KT
Morgan
Michael
M
Mott
Richard
R
Mullikin
James C
JC
Muzny
Donna M
DM
Nash
William E
WE
Nelson
Joanne O
JO
Nhan
Michael N
MN
Nicol
Robert
R
Ning
Zemin
Z
Nusbaum
Chad
C
O'Connor
Michael J
MJ
Okazaki
Yasushi
Y
Oliver
Karen
K
Overton-Larty
Emma
E
Pachter
Lior
L
Parra
Genís
G
Pepin
Kymberlie H
KH
Peterson
Jane
J
Pevzner
Pavel
P
Plumb
Robert
R
Pohl
Craig S
CS
Poliakov
Alex
A
Ponce
Tracy C
TC
Ponting
Chris P
CP
Potter
Simon
S
Quail
Michael
M
Reymond
Alexandre
A
Roe
Bruce A
BA
Roskin
Krishna M
KM
Rubin
Edward M
EM
Rust
Alistair G
AG
Santos
Ralph
R
Sapojnikov
Victor
V
Schultz
Brian
B
Schultz
Jörg
J
Schwartz
Matthias S
MS
Schwartz
Scott
S
Scott
Carol
C
Seaman
Steven
S
Searle
Steve
S
Sharpe
Ted
T
Sheridan
Andrew
A
Shownkeen
Ratna
R
Sims
Sarah
S
Singer
Jonathan B
JB
Slater
Guy
G
Smit
Arian
A
Smith
Douglas R
DR
Spencer
Brian
B
Stabenau
Arne
A
Stange-Thomann
Nicole
N
Sugnet
Charles
C
Suyama
Mikita
M
Tesler
Glenn
G
Thompson
Johanna
J
Torrents
David
D
Trevaskis
Evanne
E
Tromp
John
J
Ucla
Catherine
C
Ureta-Vidal
Abel
A
Vinson
Jade P
JP
Von Niederhausern
Andrew C
AC
Wade
Claire M
CM
Wall
Melanie
M
Weber
Ryan J
RJ
Weiss
Robert B
RB
Wendl
Michael C
MC
West
Anthony P
AP
Wetterstrand
Kris
K
Wheeler
Raymond
R
Whelan
Simon
S
Wierzbowski
Jamey
J
Willey
David
D
Williams
Sophie
S
Wilson
Richard K
RK
Winter
Eitan
E
Worley
Kim C
KC
Wyman
Dudley
D
Yang
Shan
S
Yang
Shiaw-Pyng
SP
Zdobnov
Evgeny M
EM
Zody
Michael C
MC
Lander
Eric S
ES
D000818:Animals; D001482:Base Composition; D033481:Chromosomes, Mammalian / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D005796:Genes / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D051379:Mice / Q000145:classification / Q000235:genetics*; D018345:Mice, Knockout; D008822:Mice, Transgenic; D023421:Models, Animal; D005810:Multigene Family / Q000235:genetics; D016296:Mutagenesis; D009369:Neoplasms / Q000235:genetics; D020161:Physical Chromosome Mapping; D020543:Proteome / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D012730:Sex Chromosomes / Q000235:genetics; D013045:Species Specificity; D026801:Synteny
D020543:Proteome; D022661:RNA, Untranslated