Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
Gibbs
Richard A
RA
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu
Weinstock
George M
GM
Metzker
Michael L
ML
Muzny
Donna M
DM
Sodergren
Erica J
EJ
Scherer
Steven
S
Scott
Graham
G
Steffen
David
D
Worley
Kim C
KC
Burch
Paula E
PE
Okwuonu
Geoffrey
G
Hines
Sandra
S
Lewis
Lora
L
DeRamo
Christine
C
Delgado
Oliver
O
Dugan-Rocha
Shannon
S
Miner
George
G
Morgan
Margaret
M
Hawes
Alicia
A
Gill
Rachel
R
Celera
Holt
Robert A
RA
Adams
Mark D
MD
Amanatides
Peter G
PG
Baden-Tillson
Holly
H
Barnstead
Mary
M
Chin
Soo
S
Evans
Cheryl A
CA
Ferriera
Steve
S
Fosler
Carl
C
Glodek
Anna
A
Gu
Zhiping
Z
Jennings
Don
D
Kraft
Cheryl L
CL
Nguyen
Trixie
T
Pfannkoch
Cynthia M
CM
Sitter
Cynthia
C
Sutton
Granger G
GG
Venter
J Craig
JC
Woodage
Trevor
T
Smith
Douglas
D
Lee
Hong-Mei
HM
Gustafson
Erik
E
Cahill
Patrick
P
Kana
Arnold
A
Doucette-Stamm
Lynn
L
Weinstock
Keith
K
Fechtel
Kim
K
Weiss
Robert B
RB
Dunn
Diane M
DM
Green
Eric D
ED
Blakesley
Robert W
RW
Bouffard
Gerard G
GG
De Jong
Pieter J
PJ
Osoegawa
Kazutoyo
K
Zhu
Baoli
B
Marra
Marco
M
Schein
Jacqueline
J
Bosdet
Ian
I
Fjell
Chris
C
Jones
Steven
S
Krzywinski
Martin
M
Mathewson
Carrie
C
Siddiqui
Asim
A
Wye
Natasja
N
McPherson
John
J
Zhao
Shaying
S
Fraser
Claire M
CM
Shetty
Jyoti
J
Shatsman
Sofiya
S
Geer
Keita
K
Chen
Yixin
Y
Abramzon
Sofyia
S
Nierman
William C
WC
Havlak
Paul H
PH
Chen
Rui
R
Durbin
K James
KJ
Simons
Rain
R
Ren
Yanru
Y
Song
Xing-Zhi
XZ
Li
Bingshan
B
Liu
Yue
Y
Qin
Xiang
X
Cawley
Simon
S
Worley
Kim C
KC
Cooney
A J
AJ
D'Souza
Lisa M
LM
Martin
Kirt
K
Wu
Jia Qian
JQ
Gonzalez-Garay
Manuel L
ML
Jackson
Andrew R
AR
Kalafus
Kenneth J
KJ
McLeod
Michael P
MP
Milosavljevic
Aleksandar
A
Virk
Davinder
D
Volkov
Andrei
A
Wheeler
David A
DA
Zhang
Zhengdong
Z
Bailey
Jeffrey A
JA
Eichler
Evan E
EE
Tuzun
Eray
E
Birney
Ewan
E
Mongin
Emmanuel
E
Ureta-Vidal
Abel
A
Woodwark
Cara
C
Zdobnov
Evgeny
E
Bork
Peer
P
Suyama
Mikita
M
Torrents
David
D
Alexandersson
Marina
M
Trask
Barbara J
BJ
Young
Janet M
JM
Huang
Hui
H
Wang
Huajun
H
Xing
Heming
H
Daniels
Sue
S
Gietzen
Darryl
D
Schmidt
Jeanette
J
Stevens
Kristian
K
Vitt
Ursula
U
Wingrove
Jim
J
Camara
Francisco
F
Mar Albà
M
M
Abril
Josep F
JF
Guigo
Roderic
R
Smit
Arian
A
Dubchak
Inna
I
Rubin
Edward M
EM
Couronne
Olivier
O
Poliakov
Alexander
A
Hübner
Norbert
N
Ganten
Detlev
D
Goesele
Claudia
C
Hummel
Oliver
O
Kreitler
Thomas
T
Lee
Young-Ae
YA
Monti
Jan
J
Schulz
Herbert
H
Zimdahl
Heike
H
Himmelbauer
Heinz
H
Lehrach
Hans
H
Jacob
Howard J
HJ
Bromberg
Susan
S
Gullings-Handley
Jo
J
Jensen-Seaman
Michael I
MI
Kwitek
Anne E
AE
Lazar
Jozef
J
Pasko
Dean
D
Tonellato
Peter J
PJ
Twigger
Simon
S
Ponting
Chris P
CP
Duarte
Jose M
JM
Rice
Stephen
S
Goodstadt
Leo
L
Beatson
Scott A
SA
Emes
Richard D
RD
Winter
Eitan E
EE
Webber
Caleb
C
Brandt
Petra
P
Nyakatura
Gerald
G
Adetobi
Margaret
M
Chiaromonte
Francesca
F
Elnitski
Laura
L
Eswara
Pallavi
P
Hardison
Ross C
RC
Hou
Minmei
M
Kolbe
Diana
D
Makova
Kateryna
K
Miller
Webb
W
Nekrutenko
Anton
A
Riemer
Cathy
C
Schwartz
Scott
S
Taylor
James
J
Yang
Shan
S
Zhang
Yi
Y
Lindpaintner
Klaus
K
Andrews
T Dan
TD
Caccamo
Mario
M
Clamp
Michele
M
Clarke
Laura
L
Curwen
Valerie
V
Durbin
Richard
R
Eyras
Eduardo
E
Searle
Stephen M
SM
Cooper
Gregory M
GM
Batzoglou
Serafim
S
Brudno
Michael
M
Sidow
Arend
A
Stone
Eric A
EA
Venter
J Craig
JC
Payseur
Bret A
BA
Bourque
Guillaume
G
López-Otín
Carlos
C
Puente
Xose S
XS
Chakrabarti
Kushal
K
Chatterji
Sourav
S
Dewey
Colin
C
Pachter
Lior
L
Bray
Nicolas
N
Yap
Von Bing
VB
Caspi
Anat
A
Tesler
Glenn
G
Pevzner
Pavel A
PA
Haussler
David
D
Roskin
Krishna M
KM
Baertsch
Robert
R
Clawson
Hiram
H
Furey
Terrence S
TS
Hinrichs
Angie S
AS
Karolchik
Donna
D
Kent
William J
WJ
Rosenbloom
Kate R
KR
Trumbower
Heather
H
Weirauch
Matt
M
Cooper
David N
DN
Stenson
Peter D
PD
Ma
Bin
B
Brent
Michael
M
Arumugam
Manimozhiyan
M
Shteynberg
David
D
Copley
Richard R
RR
Taylor
Martin S
MS
Riethman
Harold
H
Mudunuri
Uma
U
Peterson
Jane
J
Guyer
Mark
M
Felsenfeld
Adam
A
Old
Susan
S
Mockrin
Stephen
S
Collins
Francis
F
D000818:Animals; D001482:Base Composition; D002503:Centromere / Q000235:genetics; D033481:Chromosomes, Mammalian / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D023281:Genomics; D006801:Humans; D007438:Introns / Q000235:genetics; D008297:Male; D051379:Mice; D008958:Models, Molecular; D016296:Mutagenesis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D051381:Rats; D011914:Rats, Inbred BN / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D018626:Retroelements / Q000235:genetics; D017422:Sequence Analysis, DNA; D016615:Telomere / Q000235:genetics
D004251:DNA Transposable Elements; D004272:DNA, Mitochondrial; D022821:RNA Splice Sites; D022661:RNA, Untranslated; D018626:Retroelements