Xenopus tropicalis v3.0

Please note that this organism is for archival use only. Please see the current Xenopus tropicalis v4.1 site for the latest data and information.

Status - Releases - Collaborators - Links - Resources - Funding

Project Status

The genome of Xenopus (Silurana) tropicalis is estimated to be approximately 1.7 billion base pairs contained in 10 pairs of chromosomes, and is being sequenced to approximately 8X depth.

ATTENTION!
This site is for atrchival use only. Please see the current Xenopus tropicalis site for the latest data and information.

The assembly release v3.0 includes a total of 33,749 gene models composed of known X. tropicalis genes mapped onto genomic sequence, homology-based, and ab initio gene models. This preliminary set of gene models was created using the JGI annotation pipeline. Additional support for the predicted gene models was provided from available EST and cDNA data for X. tropicalis and X. laevis.

New annotations and browser for assembly release v.4.0 coming in August 2005.

Assembly Releases

v.4.0 (June 2005): The assembly release version 4.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.65X. After trimming for vector and quality, 22.5 Million reads assembled into 19,759 scaffolds totaling 1.51 Gbp. Roughly half of the genome is contained in 272 scaffolds all at least 1.56 Mb in length.

v.3.0 (October 2004): The assembly release version 3.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.4X. After trimming for vector and quality, 19.1 Million reads assembled into 27,064 scaffolds totaling 1.63 Gbp. Roughly half of the genome is contained in 392 scaffolds all at least 1.2 Mb in length.

Collaborators

Richard Harland , University of California at Berkeley
Rob Grainger , University of Virginia

Links

Useful links and articles: Xenopus express
Frog genetics: Xenopus tropicalis leaps into the future
Why Xenopus tropicalis? Bringing Genetics To Xenopus
An amphibian model for vertebrate developmental genetics
Importance of Xenopus tropicalis to biomedical and biological research [PDF]
Trans-NIH Xenopus initiative

Resources

The online Xenopus database, Xenbase.
University of Virginia X. tropicalis resources.
Suppliers of X. tropicalis: Xenopus I, Inc. and Xenopus Express
Sanger Institute X. tropicalis EST Project
The X. tropicalis Genome Project white paper.

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.