title: The genome of the Western clawed frog Xenopus tropicalis.
abstract: 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.
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. uhellsten@lbl.gov
authors.forename: Uffe
authors.initials: U
authors.lastname: Hellsten
authors.forename: Richard M
authors.initials: RM
authors.lastname: Harland
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: David
authors.initials: D
authors.lastname: Hendrix
authors.forename: Jerzy
authors.initials: J
authors.lastname: Jurka
authors.forename: Vladimir
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authors.lastname: Kapitonov
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
authors.forename: Nicholas H
authors.initials: NH
authors.lastname: Putnam
authors.forename: Shengqiang
authors.initials: S
authors.lastname: Shu
authors.forename: Leila
authors.initials: L
authors.lastname: Taher
authors.forename: Ira L
authors.initials: IL
authors.lastname: Blitz
authors.forename: Bruce
authors.initials: B
authors.lastname: Blumberg
authors.forename: Darwin S
authors.initials: DS
authors.lastname: Dichmann
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.forename: Enrique
authors.initials: E
authors.lastname: Amaya
authors.forename: John C
authors.initials: JC
authors.lastname: Detter
authors.forename: Russell
authors.initials: R
authors.lastname: Fletcher
authors.forename: Daniela S
authors.initials: DS
authors.lastname: Gerhard
authors.forename: David
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authors.lastname: Goodstein
authors.forename: Tina
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authors.lastname: Graves
authors.forename: Igor V
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authors.lastname: Grigoriev
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawashima
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Susan M
authors.initials: SM
authors.lastname: Lucas
authors.forename: Paul E
authors.initials: PE
authors.lastname: Mead
authors.forename: Therese
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authors.lastname: Mitros
authors.forename: Hajime
authors.initials: H
authors.lastname: Ogino
authors.forename: Yuko
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authors.lastname: Ohta
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Poliakov
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pollet
authors.forename: Jacques
authors.initials: J
authors.lastname: Robert
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Amy K
authors.initials: AK
authors.lastname: Sater
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Astrid
authors.initials: A
authors.lastname: Terry
authors.forename: Peter D
authors.initials: PD
authors.lastname: Vize
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.forename: Dan
authors.initials: D
authors.lastname: Wells
authors.forename: Andrea
authors.initials: A
authors.lastname: Wills
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: Lyle B
authors.initials: LB
authors.lastname: Zimmerman
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Zorn
authors.forename: Robert
authors.initials: R
authors.lastname: Grainger
authors.forename: Timothy
authors.initials: T
authors.lastname: Grammer
authors.forename: Mustafa K
authors.initials: MK
authors.lastname: Khokha
authors.forename: Paul M
authors.initials: PM
authors.lastname: Richardson
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
mesh_terms: 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
chemical_list: D004251:DNA Transposable Elements; D018076:DNA, Complementary; D029867:Xenopus Proteins