The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.
The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
Dehal
Paramvir
P
U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
Satou
Yutaka
Y
Campbell
Robert K
RK
Chapman
Jarrod
J
Degnan
Bernard
B
De Tomaso
Anthony
A
Davidson
Brad
B
Di Gregorio
Anna
A
Gelpke
Maarten
M
Goodstein
David M
DM
Harafuji
Naoe
N
Hastings
Kenneth E M
KE
Ho
Isaac
I
Hotta
Kohji
K
Huang
Wayne
W
Kawashima
Takeshi
T
Lemaire
Patrick
P
Martinez
Diego
D
Meinertzhagen
Ian A
IA
Necula
Simona
S
Nonaka
Masaru
M
Putnam
Nik
N
Rash
Sam
S
Saiga
Hidetoshi
H
Satake
Masanobu
M
Terry
Astrid
A
Yamada
Lixy
L
Wang
Hong-Gang
HG
Awazu
Satoko
S
Azumi
Kaoru
K
Boore
Jeffrey
J
Branno
Margherita
M
Chin-Bow
Stephen
S
DeSantis
Rosaria
R
Doyle
Sharon
S
Francino
Pilar
P
Keys
David N
DN
Haga
Shinobu
S
Hayashi
Hiroko
H
Hino
Kyosuke
K
Imai
Kaoru S
KS
Inaba
Kazuo
K
Kano
Shungo
S
Kobayashi
Kenji
K
Kobayashi
Mari
M
Lee
Byung-In
BI
Makabe
Kazuhiro W
KW
Manohar
Chitra
C
Matassi
Giorgio
G
Medina
Monica
M
Mochizuki
Yasuaki
Y
Mount
Steve
S
Morishita
Tomomi
T
Miura
Sachiko
S
Nakayama
Akie
A
Nishizaka
Satoko
S
Nomoto
Hisayo
H
Ohta
Fumiko
F
Oishi
Kazuko
K
Rigoutsos
Isidore
I
Sano
Masako
M
Sasaki
Akane
A
Sasakura
Yasunori
Y
Shoguchi
Eiichi
E
Shin-i
Tadasu
T
Spagnuolo
Antoinetta
A
Stainier
Didier
D
Suzuki
Miho M
MM
Tassy
Olivier
O
Takatori
Naohito
N
Tokuoka
Miki
M
Yagi
Kasumi
K
Yoshizaki
Fumiko
F
Wada
Shuichi
S
Zhang
Cindy
C
Hyatt
P Douglas
PD
Larimer
Frank
F
Detter
Chris
C
Doggett
Norman
N
Glavina
Tijana
T
Hawkins
Trevor
T
Richardson
Paul
P
Lucas
Susan
S
Kohara
Yuji
Y
Levine
Michael
M
Satoh
Nori
N
Rokhsar
Daniel S
DS
D000483:Alleles; D000818:Animals; D017209:Apoptosis; D001483:Base Sequence; D002482:Cellulose / Q000378:metabolism; D002490:Central Nervous System / Q000502:physiology; D002938:Ciona intestinalis / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics* / Q000502:physiology; D019295:Computational Biology; D004703:Endocrine System / Q000502:physiology; D018628:Gene Dosage; D020440:Gene Duplication; D005796:Genes; D005801:Genes, Homeobox; D016678:Genome; D006321:Heart / Q000196:embryology / Q000502:physiology; D007109:Immunity / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D009124:Muscle Proteins / Q000235:genetics; D020897:Organizers, Embryonic / Q000502:physiology; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011506:Proteins / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013961:Thyroid Gland / Q000502:physiology; D014561:Urochordata / Q000235:genetics; D014714:Vertebrates / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics / Q000502:physiology
D009124:Muscle Proteins; D011506:Proteins; D002482:Cellulose