Early cell fate decisions, body plan patterning and early organogenesis are processes where Xenopus proved to be a good model. Indeed, Xenopus was the first cloned vertebrate animal. Contributions in cell biology and biochemistry include seminal work on chromosome replication, chromatin and nuclear assembly, control of the cell cycle, in vitro reconstruction of cytoskeletal dynamics, and signalling pathways. Late development at metamorphosis and its hormonal control provides another fruitful research area pertinent to human disease. Xenopus has become an appreciated model for ontogenetic and phylogenetic studies of immunity. Finally, embryos and tadpoles are used in toxicological testing worldwide.
We know a lot on Xenopus development, but its genome is still poorly characterized. This is due to its large size. Amphibians are well known as an example of the C paradox, and Xenopus is no exception to this. X. laevis has a long generation time and is pseudo-tetraploid, thereby hindering genetic analyses. X. tropicalis, which is diploid and has a shorter generation time, is attracting increasing interest.
In the literature, the terms african clawed frog and Xenopus refer most often to Xenopus laevis laevis. However, the X. laevis group alone includes six morphologically distinct subspecies of which X. laevis laevis is but one. A total of 17 Xenopus and Silurana species have been identified and together compose the Xenopodinae subfamily of Pipidae (tongueless frogs with a principal aquatic life). Here we refer to the preferred scientific name Xenopus tropicalis and not Silurana tropicalis (the same applies for X. epitropicalis). Remarkably, it was established that these Xenopus species form a polyploidy series, from the diploid (2n) X. tropicalis to the dodecaploÃ¯d (12n) X. ruwensoriensis. These different levels of ploidy are due to interspecific hybridization events that took place over a period ranging from 30 to 55 million years ago. Hence all but one Xenopus species are allopolyploids.
X. tropicalis presents the same advantages as the X. laevis species but it is diploid and has a smaller genome (1.7 vs 3.1 Gbp), and a shorter generation time (5 and 9 months for males and females, respectively). Thus, scientists interested in amphibian genome characteristics preferred to decipher the genome of X. tropicalis. Fortunately, most of the work done previously on X. laevis is directly exploitable on X. tropicalis. However, some gene products are not as conserved as others and nucleic probes for homologous genes may even not cross-hybridize between the two species.
Since X. tropicalis is diploid it has the potential to become a better model in developmental genetics than X. laevis (pseudotetraploid) and zebrafish (duplicated genome). Important genomic resources are underway: physical and genomic map, cDNA collections and genome sequencing.
The 1.7 Gbp haploid genome of X. tropicalis is divided among 10 chromosomes.
The genome of an F6 and an F7 inbred Nigerian female X. tropicalis was sequenced at 8X depth using a whole genome shotgun approach by the Joint Genome Institute from the U.S.A Department of Energy.
The JGI annotation pipeline predicted approximately 28,000 gene models. Only 55 % of these have support from available X. tropicalis and X. laevis EST and cDNA data. On the other hand, an estimated 5 % of cDNA sequences are not mapped on the genome assembly.