The Genome of the Western Clawed Frog Xenopus tropicalis
By U. Hellsten, R. Harland, M. Gilchrist, David A. Hendrix, Jerzy Jurka, Vladimir V. Kapitonov, Ivan Ovcharenko, Nicholas H. Putnam, S. Shu, L. Taher and 38 more. Science, 2010
828 citations recorded by the source corpus.
Frog Genome The African clawed frog Xenopus tropicalis is the first amphibian to have its genome sequenced. Hellsten et al. (p. 633, see the cover) present an analysis of a draft assembly of the genome. The genome of the frog, which is an important model system for developmental biology, encodes over 20,000 protein-coding genes, of which more than 1700 genes have identified human disease associations. Detailed comparison of the content of protein-coding genes with other tetrapods—human and chicken—reveals extensive shared synteny, occasionally spanning entire chromosomes. Assembly, annotation, and analysis of the frog genome compares gene content and synteny with the human and chicken genomes. 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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/9909e6a0a2bc6dc1dcff373f37a406dd43b21214
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In Molecular Biology
Citations in the corpus
- Species Delimitation in Herpetology (2019, neutral): “…(e.g.: Alligator: Wan et al., 2013; Ambystoma: Nowoshilow et al., 2018; Anolis: Alföldi et al., 2011; Chelonia and Pelodiscus: Wang et al., 2014; Nanorana: Sun et al., 2015; Ophiophagus: Vonk et al., 2013; Python: Castoe et al., 2013; Thermophis: Li et al., 2018; Xenopus: Hellston et al., 2010).”
- Genome duplication in amphibians and fish: an extended synthesis (2011, background): “The first amphibian genome sequence has recently been published (Hellsten et al., 2010) (described as Xenopus tropicalis rather than Si. tropicalis) but no tetraploids have yet been sequenced.”
- Determinants and Consequences of Dispersal in Vertebrates with Complex Life Cycles: A Review of Pond-Breeding Amphibians (2018, background): “2018b), and the genomes of some species are well described (Hellsten et al. 2010; Edwards et al. 2018;Nowoshilowet al. 2018).”