Xenopus Genome Project
Xenopus laevis is an essential model organism in several areas of biology (see Harland & Grainger, TIG (2011) for review). 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 obtained funding from the Texas Institute for Drug and Diagnostic Development (TI3D), in conjunction with projects funded by the National Institutes of Health, to begin sequencing of the X. laevis genome. We began the project 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.
The project rapidly expanded to include de novo reconstruction of X. laevis transcripts, in collaboration with groups around the world donating Illumina Hi-Seq RNA sequencing datasets, coordinating these efforts with genome sequencing by the Harland and Rokhsar groups at UC Berkeley and with Taira and collaborators at the University of Tokyo, Japan. We're posting our intermediate datasets here in advance of publication for use by the wider community.
If you have any question about this data in general, please contact Taejoon Kwon.
You can download X. laevis genomes at XenBase FTP site. Alternatively, you can download them at UTA 'daudin' web repository. Current version is called 'JGI 7.1' at XenBase, and 'JGIv7b' at UTA web repository('daudin'). See XENLA_Genome page for detailed info for each version.
- http://daudin.icmb.utexas.edu (MayBall)
- If you want to search on Oktoberfest version, go to http://daudin.icmb.utexas.edu/Oktoberfest/
If you are looking for assembled transcripts per dataset (that I posted before releasing Oktoberfest gene model), see http://daudin.icmb.utexas.edu/pub/tx/final.2012sep/ TaejoonKwon (talk) 17:30, 8 January 2014 (CST)
- XENLA_Oktoberfest - released on October, 2012 (code name "Oktoberfest")
- XENLA_Mayball - released on May, 2013 (code name "MayBall")
CHORI-219 BAC sequencing
We started the first runs by sequencing 96 BACs from the CHORI-219 library (vector: pBACGK1.1) at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc., as initially identified by the group of Jan-Fang Cheng via probing the CHORI-219 library), as well as 10 BACs that have already been sequenced by the DOE Joint Genome Institute/HudsonAlpha Genome Sequencing Center to serve as positive controls for the sequencing and assembly pipeline.
- CHORI-219 BACs: List of 96 test BACs (MS Excel file)
See /XENLA_SA09023 for more details. 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 by raw data, ~50X coverage by high quality data, of the BAC set.
- Given that we currently see better mapping of the shotgun SA09023 reads to X. tropicalis than to X. laevis (both to BACs and mRNAs), we're confirming the sample identity before continuing with whole genome sequencing. See the 'sanity check' /Species_Identification for details.
J-strain whole genome sequencing
In addition, we are generating several mate pair libraries of different sizes from genomic DNA prepared by Mustafa Khokha from J strain frogs obtained from Jacques Robert, 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.
- TXGP_RNAseq_assembly - Current status of TXGP
- XENLA_Genome - Current status of Xenopus genome
- TXGP_reference - Public resources compiled to be used in TXGP.
- TXGP_ens63_reference - Some statistics derived from EnsEMBL-63 (used as a reference in TXGP).
- TXGP_Data_Description - Data collected in TXGP.