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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.

SUBMITTER: Hellsten U 

PROVIDER: S-EPMC2994648 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature

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The genome of the Western clawed frog Xenopus tropicalis.

Hellsten Uffe U   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  

Science (New York, N.Y.) 20100401 5978

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 tra  ...[more]

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