Difference between revisions of "Xenopus Genome Project"

Revision as of 19:44, 20 November 2009

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 regions, and for design of morpholino-oligonucleotides for gene knockdowns.

The Wallingford and Marcotte labs have obtained funding from the Texas Institute for Drug and Diagnostic Development (TI3D) to begin sequencing of the X. laevis genome. We are primarily working with Scott Hunicke-Smith at the University of Texas Genome Sequencing and Analysis facility, with funding sufficient for ~20x coverage of the X. laevis genome using ABI SOLiD next-generation sequencing. 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.

Progress Reports

List of 96 test BACs

11/16/2009 - First test stage of sequencing done! Three mate paired libraries were sequenced:
X_laevis_WG - the X. laevis whole genome library, 5kb insert size - about 4.4GB raw data, 0.4GB high quality data
X_laevis_2kb - The set of 96 BACs, with 2kb insert size - about 3.6GB raw data, 0.3GB high quality data
X_laevis_5kb - The set of 96 BACs, with 5kb insert size - about 2.8GB raw data, 0.2GB high quality data
This (very roughly) corresponds to >600X coverage raw data, ~50X coverage high quality data of the BAC set.