Xenopus Genome Project
The Texas Xenopus Genome Project
Xenopus laevis is an essential model organism in several areas of biology. In addition to the key attributes of these embryos for in vivo imaging, cell-free extracts from Xenopus provide among the most powerful in vitro systems for studies of cell and molecular biology. A complete sequence of the X. laevis genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory region, and for design of morpholino-oligonucleotides for gene knockdowns.
The Wallingford and Marcotte labs have now obtained funding to begin sequencing of the X. laevis genome from the Texas Institute for Drug and Diagnostic Development (TI3D). We are primarily using the ABI SOLiD next-generation sequencing facility at UT, Austin, with funding sufficient for ~20x coverage of the X. laevis genome. We have started the first runs by sequencing 96 BACs from the CHORI-219 library at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc.), as well as 10 BACs that have already been sequenced by HudsonAlpha to serve as positive controls for the sequencing and assembly pipeline. In addition, we are generating several mate pair libraries of different sizes from genomic DNA from J strain frogs (obtained from Jacques Robert via Mustafa Khokha), sequencing each to multiple-fold coverage of the genome.
The primary data from this project will be made available as soon as possible for use by the community. We plan to periodically post reports on our progress below.