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.

Fig. 1

Comparison of adults and tadpoles of X.tropicalis and X. laevis. Adult body length is 5 and 10 cm respectively. (A) tailbud (B) swimming tadpole (C) feeding tadpole. White bar indicates 1 mm.

Figure 2

Blocks of conserved tetrapod linkage for human (panel A) and chicken (panel B) chromosome 1 reveal fusions (solid black triangles) and break points (unfilled triangles) in amniotes. A total of three human fusions (panel A), seven human breaks (panel B), and one chicken fusion (panel B) is observed. The green triangle in panel B indicates the position of an apparent frog-specific break or ancestral amniote fusion. Grey areas indicate origin in different ancestral chromosomes. Shaded areas show larger regions with insufficient three-way synteny information. Detailed comparison of gene order in human and chicken reveals multiple large-scale inversions (dot plots on the black blocks). The green frog blocks consist of multiple scaffolds, 55 in panel A and 97 in panel B. Bars on the frog blocks show the location of scaffolds which do not contain markers from the linkage map, but have been predicted to associate with the linkage group by conserved synteny.