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Open Access Publications from the University of California

Chapter 2: The Xenopus tropicalis genome project

  • Author(s): Richardson, Paul M.
  • Chapman, Jarrod
  • et al.

The Human Genome Project has resulted in the elucidation of the genomic sequence of a number of model organisms as well as a reference sequence for the human genome. The utility of these available genomes has been demonstrated by researchers throughout the world, and spurred the desire to obtain additional genomic information from a number of sources. The United States Department of Energy s Joint Genome Institute has undertaken a project to sequence the genome of the amphibian Xenopus (Silurana) tropicalis. The primary goal of the project is to produce a high-quality genome sequence and annotation to meet the needs of the research community. In March of 2002, a number of Xenopus researchers from around the world met at the JGI Production Genomics Facility in Walnut Creek, California to discuss goals and strategies for the project. The project is designed to make use of a whole-genome shotgun approach supplemented with extensive BAC end sequences and shotgun sequence from selected BACs. A high-quality draft genome is desired that will meet minimal criteria for contiguity and long-range linking information. At depths of 6-8X sequence coverage, we expect that a large fraction of features of interest (exons, promoters and regulatory regions) will be covered in large contigs of high sequence quality without gaps. In addition, long-range linking of contigs will be achieved through paired end gap-spanning clones so that contigs are ordered and oriented into large scaffolds with gaps of defined size. These scaffolds typically contain multi megabase-sized regions of the genome. This approach has led to high-quality draft genomes of the pufferfish (Fugu rubripes), Ciona intestinalis and the mouse. Since there will be extensive coverage of large inserts for Xenopus including BAC and Fosmid end sequencing, clones will be readily available for finishing selected regions of the genome.

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