The genome of the sea urchin Strongylocentrotus purpuratus.
We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
Sodergren
Erica
E
Weinstock
George M
GM
Davidson
Eric H
EH
Cameron
R Andrew
RA
Gibbs
Richard A
RA
Angerer
Robert C
RC
Angerer
Lynne M
LM
Arnone
Maria Ina
MI
Burgess
David R
DR
Burke
Robert D
RD
Coffman
James A
JA
Dean
Michael
M
Elphick
Maurice R
MR
Ettensohn
Charles A
CA
Foltz
Kathy R
KR
Hamdoun
Amro
A
Hynes
Richard O
RO
Klein
William H
WH
Marzluff
William
W
McClay
David R
DR
Morris
Robert L
RL
Mushegian
Arcady
A
Rast
Jonathan P
JP
Smith
L Courtney
LC
Thorndyke
Michael C
MC
Vacquier
Victor D
VD
Wessel
Gary M
GM
Wray
Greg
G
Zhang
Lan
L
Elsik
Christine G
CG
Ermolaeva
Olga
O
Hlavina
Wratko
W
Hofmann
Gretchen
G
Kitts
Paul
P
Landrum
Melissa J
MJ
Mackey
Aaron J
AJ
Maglott
Donna
D
Panopoulou
Georgia
G
Poustka
Albert J
AJ
Pruitt
Kim
K
Sapojnikov
Victor
V
Song
Xingzhi
X
Souvorov
Alexandre
A
Solovyev
Victor
V
Wei
Zheng
Z
Whittaker
Charles A
CA
Worley
Kim
K
Durbin
K James
KJ
Shen
Yufeng
Y
Fedrigo
Olivier
O
Garfield
David
D
Haygood
Ralph
R
Primus
Alexander
A
Satija
Rahul
R
Severson
Tonya
T
Gonzalez-Garay
Manuel L
ML
Jackson
Andrew R
AR
Milosavljevic
Aleksandar
A
Tong
Mark
M
Killian
Christopher E
CE
Livingston
Brian T
BT
Wilt
Fred H
FH
Adams
Nikki
N
Bellé
Robert
R
Carbonneau
Seth
S
Cheung
Rocky
R
Cormier
Patrick
P
Cosson
Bertrand
B
Croce
Jenifer
J
Fernandez-Guerra
Antonio
A
Genevière
Anne-Marie
AM
Goel
Manisha
M
Kelkar
Hemant
H
Morales
Julia
J
Mulner-Lorillon
Odile
O
Robertson
Anthony J
AJ
Goldstone
Jared V
JV
Cole
Bryan
B
Epel
David
D
Gold
Bert
B
Hahn
Mark E
ME
Howard-Ashby
Meredith
M
Scally
Mark
M
Stegeman
John J
JJ
Allgood
Erin L
EL
Cool
Jonah
J
Judkins
Kyle M
KM
McCafferty
Shawn S
SS
Musante
Ashlan M
AM
Obar
Robert A
RA
Rawson
Amanda P
AP
Rossetti
Blair J
BJ
Gibbons
Ian R
IR
Hoffman
Matthew P
MP
Leone
Andrew
A
Istrail
Sorin
S
Materna
Stefan C
SC
Samanta
Manoj P
MP
Stolc
Viktor
V
Tongprasit
Waraporn
W
Tu
Qiang
Q
Bergeron
Karl-Frederik
KF
Brandhorst
Bruce P
BP
Whittle
James
J
Berney
Kevin
K
Bottjer
David J
DJ
Calestani
Cristina
C
Peterson
Kevin
K
Chow
Elly
E
Yuan
Qiu Autumn
QA
Elhaik
Eran
E
Graur
Dan
D
Reese
Justin T
JT
Bosdet
Ian
I
Heesun
Shin
S
Marra
Marco A
MA
Schein
Jacqueline
J
Anderson
Michele K
MK
Brockton
Virginia
V
Buckley
Katherine M
KM
Cohen
Avis H
AH
Fugmann
Sebastian D
SD
Hibino
Taku
T
Loza-Coll
Mariano
M
Majeske
Audrey J
AJ
Messier
Cynthia
C
Nair
Sham V
SV
Pancer
Zeev
Z
Terwilliger
David P
DP
Agca
Cavit
C
Arboleda
Enrique
E
Chen
Nansheng
N
Churcher
Allison M
AM
Hallböök
F
F
Humphrey
Glen W
GW
Idris
Mohammed M
MM
Kiyama
Takae
T
Liang
Shuguang
S
Mellott
Dan
D
Mu
Xiuqian
X
Murray
Greg
G
Olinski
Robert P
RP
Raible
Florian
F
Rowe
Matthew
M
Taylor
John S
JS
Tessmar-Raible
Kristin
K
Wang
D
D
Wilson
Karen H
KH
Yaguchi
Shunsuke
S
Gaasterland
Terry
T
Galindo
Blanca E
BE
Gunaratne
Herath J
HJ
Juliano
Celina
C
Kinukawa
Masashi
M
Moy
Gary W
GW
Neill
Anna T
AT
Nomura
Mamoru
M
Raisch
Michael
M
Reade
Anna
A
Roux
Michelle M
MM
Song
Jia L
JL
Su
Yi-Hsien
YH
Townley
Ian K
IK
Voronina
Ekaterina
E
Wong
Julian L
JL
Amore
Gabriele
G
Branno
Margherita
M
Brown
Euan R
ER
Cavalieri
Vincenzo
V
Duboc
Véronique
V
Duloquin
Louise
L
Flytzanis
Constantin
C
Gache
Christian
C
Lapraz
François
F
Lepage
Thierry
T
Locascio
Annamaria
A
Martinez
Pedro
P
Matassi
Giorgio
G
Matranga
Valeria
V
Range
Ryan
R
Rizzo
Francesca
F
Röttinger
Eric
E
Beane
Wendy
W
Bradham
Cynthia
C
Byrum
Christine
C
Glenn
Tom
T
Hussain
Sofia
S
Manning
Gerard
G
Miranda
Esther
E
Thomason
Rebecca
R
Walton
Katherine
K
Wikramanayke
Athula
A
Wu
Shu-Yu
SY
Xu
Ronghui
R
Brown
C Titus
CT
Chen
Lili
L
Gray
Rachel F
RF
Lee
Pei Yun
PY
Nam
Jongmin
J
Oliveri
Paola
P
Smith
Joel
J
Muzny
Donna
D
Bell
Stephanie
S
Chacko
Joseph
J
Cree
Andrew
A
Curry
Stacey
S
Davis
Clay
C
Dinh
Huyen
H
Dugan-Rocha
Shannon
S
Fowler
Jerry
J
Gill
Rachel
R
Hamilton
Cerrissa
C
Hernandez
Judith
J
Hines
Sandra
S
Hume
Jennifer
J
Jackson
Laronda
L
Jolivet
Angela
A
Kovar
Christie
C
Lee
Sandra
S
Lewis
Lora
L
Miner
George
G
Morgan
Margaret
M
Nazareth
Lynne V
LV
Okwuonu
Geoffrey
G
Parker
David
D
Pu
Ling-Ling
LL
Thorn
Rachel
R
Wright
Rita
R
D000818:Animals; D002113:Calcification, Physiologic; D015815:Cell Adhesion Molecules / Q000235:genetics / Q000502:physiology; D003167:Complement Activation / Q000235:genetics; D019295:Computational Biology; D047108:Embryonic Development / Q000235:genetics; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D005796:Genes; D016678:Genome; D007113:Immunity, Innate / Q000235:genetics; D007155:Immunologic Factors / Q000235:genetics / Q000502:physiology; D008297:Male; D009424:Nervous System Physiological Phenomena; D011506:Proteins / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA; D015398:Signal Transduction; D047270:Strongylocentrotus purpuratus / Q000196:embryology / Q000235:genetics* / Q000276:immunology / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics
D015815:Cell Adhesion Molecules; D007155:Immunologic Factors; D011506:Proteins; D014157:Transcription Factors