The genome of the Western clawed frog Xenopus tropicalis.
The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.
Hellsten
Uffe
U
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. uhellsten@lbl.gov
Harland
Richard M
RM
Gilchrist
Michael J
MJ
Hendrix
David
D
Jurka
Jerzy
J
Kapitonov
Vladimir
V
Ovcharenko
Ivan
I
Putnam
Nicholas H
NH
Shu
Shengqiang
S
Taher
Leila
L
Blitz
Ira L
IL
Blumberg
Bruce
B
Dichmann
Darwin S
DS
Dubchak
Inna
I
Amaya
Enrique
E
Detter
John C
JC
Fletcher
Russell
R
Gerhard
Daniela S
DS
Goodstein
David
D
Graves
Tina
T
Grigoriev
Igor V
IV
Grimwood
Jane
J
Kawashima
Takeshi
T
Lindquist
Erika
E
Lucas
Susan M
SM
Mead
Paul E
PE
Mitros
Therese
T
Ogino
Hajime
H
Ohta
Yuko
Y
Poliakov
Alexander V
AV
Pollet
Nicolas
N
Robert
Jacques
J
Salamov
Asaf
A
Sater
Amy K
AK
Schmutz
Jeremy
J
Terry
Astrid
A
Vize
Peter D
PD
Warren
Wesley C
WC
Wells
Dan
D
Wills
Andrea
A
Wilson
Richard K
RK
Zimmerman
Lyle B
LB
Zorn
Aaron M
AM
Grainger
Robert
R
Grammer
Timothy
T
Khokha
Mustafa K
MK
Richardson
Paul M
PM
Rokhsar
Daniel S
DS
D000818:Animals; D002645:Chickens / Q000235:genetics; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D004251:DNA Transposable Elements; D018076:DNA, Complementary; D004625:Embryo, Nonmammalian / Q000378:metabolism; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D020440:Gene Duplication; D005796:Genes; D016678:Genome; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D026801:Synteny; D014714:Vertebrates / Q000235:genetics; D014981:Xenopus / Q000196:embryology / Q000235:genetics*; D029867:Xenopus Proteins / Q000235:genetics
D004251:DNA Transposable Elements; D018076:DNA, Complementary; D029867:Xenopus Proteins