The genome of the Western clawed frog Xenopus tropicalis

Uffe Hellsten, Richard M Harland, Michael J Gilchrist, David Hendrix, Jerzy Jurka, Vladimir Kapitonov, Ivan Ovcharenko, Nicholas H Putnam, Shengqiang Shu, Leila Taher, Ira L Blitz, Bruce Blumberg, Darwin S Dichmann, Inna Dubchak, Enrique Amaya, John C Detter, Russell Fletcher, Daniela S Gerhard, David Goodstein, Tina Graves & 28 others Igor V Grigoriev, Jane Grimwood, Takeshi Kawashima, Erika Lindquist, Susan M Lucas, Paul E Mead, Therese Mitros, Hajime Ogino, Yuko Ohta, Alexander V Poliakov, Nicolas Pollet, Jacques Robert, Asaf Salamov, Amy K Sater, Jeremy Schmutz, Astrid Terry, Peter D Vize, Wesley C Warren, Dan Wells, Andrea Wills, Richard K Wilson, Lyle B Zimmerman, Aaron M Zorn, Robert Grainger, Timothy Grammer, Mustafa K Khokha, Paul M Richardson, Daniel S Rokhsar

Research output: Contribution to journalArticleResearchpeer-review

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.

Original languageEnglish
Pages (from-to)633-6
Number of pages4
JournalScience
Volume328
Issue number5978
DOIs
Publication statusPublished - 30 Apr 2010

Keywords

  • Animals
  • Chickens/genetics
  • Chromosome Mapping
  • Chromosomes/genetics
  • Computational Biology
  • Conserved Sequence
  • DNA Transposable Elements
  • DNA, Complementary
  • Embryo, Nonmammalian/metabolism
  • Evolution, Molecular
  • Expressed Sequence Tags
  • Gene Duplication
  • Genes
  • Genome
  • Humans
  • Phylogeny
  • Sequence Analysis, DNA
  • Synteny
  • Vertebrates/genetics
  • Xenopus/embryology
  • Xenopus Proteins/genetics

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  • Cite this

    Hellsten, U., Harland, R. M., Gilchrist, M. J., Hendrix, D., Jurka, J., Kapitonov, V., ... Rokhsar, D. S. (2010). The genome of the Western clawed frog Xenopus tropicalis. Science, 328(5978), 633-6. https://doi.org/10.1126/science.1183670