Evolutionary and biomedical insights from the rhesus macaque genome.
The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. agibbs@bcm.edu
Gibbs
Richard A
RA
Rogers
Jeffrey
J
Katze
Michael G
MG
Bumgarner
Roger
R
Weinstock
George M
GM
Mardis
Elaine R
ER
Remington
Karin A
KA
Strausberg
Robert L
RL
Venter
J Craig
JC
Wilson
Richard K
RK
Batzer
Mark A
MA
Bustamante
Carlos D
CD
Eichler
Evan E
EE
Hahn
Matthew W
MW
Hardison
Ross C
RC
Makova
Kateryna D
KD
Miller
Webb
W
Milosavljevic
Aleksandar
A
Palermo
Robert E
RE
Siepel
Adam
A
Sikela
James M
JM
Attaway
Tony
T
Bell
Stephanie
S
Bernard
Kelly E
KE
Buhay
Christian J
CJ
Chandrabose
Mimi N
MN
Dao
Marvin
M
Davis
Clay
C
Delehaunty
Kimberly D
KD
Ding
Yan
Y
Dinh
Huyen H
HH
Dugan-Rocha
Shannon
S
Fulton
Lucinda A
LA
Gabisi
Ramatu Ayiesha
RA
Garner
Toni T
TT
Godfrey
Jennifer
J
Hawes
Alicia C
AC
Hernandez
Judith
J
Hines
Sandra
S
Holder
Michael
M
Hume
Jennifer
J
Jhangiani
Shalini N
SN
Joshi
Vandita
V
Khan
Ziad Mohid
ZM
Kirkness
Ewen F
EF
Cree
Andrew
A
Fowler
R Gerald
RG
Lee
Sandra
S
Lewis
Lora R
LR
Li
Zhangwan
Z
Liu
Yih-Shin
YS
Moore
Stephanie M
SM
Muzny
Donna
D
Nazareth
Lynne V
LV
Ngo
Dinh Ngoc
DN
Okwuonu
Geoffrey O
GO
Pai
Grace
G
Parker
David
D
Paul
Heidie A
HA
Pfannkoch
Cynthia
C
Pohl
Craig S
CS
Rogers
Yu-Hui
YH
Ruiz
San Juana
SJ
Sabo
Aniko
A
Santibanez
Jireh
J
Schneider
Brian W
BW
Smith
Scott M
SM
Sodergren
Erica
E
Svatek
Amanda F
AF
Utterback
Teresa R
TR
Vattathil
Selina
S
Warren
Wesley
W
White
Courtney Sherell
CS
Chinwalla
Asif T
AT
Feng
Yucheng
Y
Halpern
Aaron L
AL
Hillier
Ladeana W
LW
Huang
Xiaoqiu
X
Minx
Pat
P
Nelson
Joanne O
JO
Pepin
Kymberlie H
KH
Qin
Xiang
X
Sutton
Granger G
GG
Venter
Eli
E
Walenz
Brian P
BP
Wallis
John W
JW
Worley
Kim C
KC
Yang
Shiaw-Pyng
SP
Jones
Steven M
SM
Marra
Marco A
MA
Rocchi
Mariano
M
Schein
Jacqueline E
JE
Baertsch
Robert
R
Clarke
Laura
L
Csürös
Miklós
M
Glasscock
Jarret
J
Harris
R Alan
RA
Havlak
Paul
P
Jackson
Andrew R
AR
Jiang
Huaiyang
H
Liu
Yue
Y
Messina
David N
DN
Shen
Yufeng
Y
Song
Henry Xing-Zhi
HX
Wylie
Todd
T
Zhang
Lan
L
Birney
Ewan
E
Han
Kyudong
K
Konkel
Miriam K
MK
Lee
Jungnam
J
Smit
Arian F A
AF
Ullmer
Brygg
B
Wang
Hui
H
Xing
Jinchuan
J
Burhans
Richard
R
Cheng
Ze
Z
Karro
John E
JE
Ma
Jian
J
Raney
Brian
B
She
Xinwei
X
Cox
Michael J
MJ
Demuth
Jeffery P
JP
Dumas
Laura J
LJ
Han
Sang-Gook
SG
Hopkins
Janet
J
Karimpour-Fard
Anis
A
Kim
Young H
YH
Pollack
Jonathan R
JR
Vinar
Tomas
T
Addo-Quaye
Charles
C
Degenhardt
Jeremiah
J
Denby
Alexandra
A
Hubisz
Melissa J
MJ
Indap
Amit
A
Kosiol
Carolin
C
Lahn
Bruce T
BT
Lawson
Heather A
HA
Marklein
Alison
A
Nielsen
Rasmus
R
Vallender
Eric J
EJ
Clark
Andrew G
AG
Ferguson
Betsy
B
Hernandez
Ryan D
RD
Hirani
Kashif
K
Kehrer-Sawatzki
Hildegard
H
Kolb
Jessica
J
Patil
Shobha
S
Pu
Ling-Ling
LL
Ren
Yanru
Y
Smith
David Glenn
DG
Wheeler
David A
DA
Schenck
Ian
I
Ball
Edward V
EV
Chen
Rui
R
Cooper
David N
DN
Giardine
Belinda
B
Hsu
Fan
F
Kent
W James
WJ
Lesk
Arthur
A
Nelson
David L
DL
O'brien
William E
WE
Prüfer
Kay
K
Stenson
Peter D
PD
Wallace
James C
JC
Ke
Hui
H
Liu
Xiao-Ming
XM
Wang
Peng
P
Xiang
Andy Peng
AP
Yang
Fan
F
Barber
Galt P
GP
Haussler
David
D
Karolchik
Donna
D
Kern
Andy D
AD
Kuhn
Robert M
RM
Smith
Kayla E
KE
Zwieg
Ann S
AS
D000818:Animals; D035843:Biomedical Research; D019143:Evolution, Molecular; D005260:Female; D020440:Gene Duplication; D015321:Gene Rearrangement; D030342:Genetic Diseases, Inborn; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D008253:Macaca mulatta / Q000235:genetics*; D008297:Male; D005810:Multigene Family; D009154:Mutation; D002679:Pan troglodytes / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity