Research on Xenopus has provided numerous new insights into cell and developmental biology. The eggs are readily manipulated by microsurgery and microinjection, and with their large size and abundance, either normal or manipulated eggs provide excellent material for biochemical and cell biological analysis. In order to make Xenopus useful for the modern age of "systems biology" where proteomic and genomic analyses promise a comprehensive understanding of life's processes, a high quality assembly of the Xenopus genome is needed. A high quality genome structure will provide a comprehensive catalog of gene content and proteome, authoritative data on conservation of chromosome structure with other vertebrates, and will improve regions of mis-assembly, bringing short scaffold regions into a chromosome-scale assembly. This proposal builds on the previous high quality draft genome assembly produced at the Department of Energy's Joint Genome Institute. While the quality is good in gene-rich regions, the long-range assembly of the genome is not as good as that for other tetrapods. This proposal will bypass the previous difficulties in assembling over the long range, by avoiding cloning-based methods of sequence mapping and long-range assembly. Instead we will use high throughput DNA sequencing and statistically based map assembly to generate a physical and genetic map, incorporating newly identified Single Nucleotide Polymorphisms (SNPs) and previously identified Simple sequence length polymorphisms (SSLPs). We will provide support for genome annotation by Metazome and Xenbase and ensure that the resources are made widely available.

Public Health Relevance

Work on model organisms has allowed the discovery of many fundamental properties of animals, and thereby allowed new insights into how human embryos develop and function. Xenopus offers large embryos that develop outside the mother, which has enabled discoveries on cell proliferation and many developmental events. The genome structure and full gene set will permit new genes and functions to be identified, functions that are highly relevant to human development and disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM086321-04
Application #
8205010
Study Section
Special Emphasis Panel (ZRG1-GGG-T (52))
Program Officer
Hoodbhoy, Tanya
Project Start
2009-01-01
Project End
2013-12-31
Budget Start
2012-01-01
Budget End
2013-12-31
Support Year
4
Fiscal Year
2012
Total Cost
$267,664
Indirect Cost
$90,226
Name
University of California Berkeley
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Jiang, Zhihua; Michal, Jennifer J; Beckman, Kenneth B et al. (2011) Development and initial characterization of a HAPPY panel for mapping the X. tropicalis genome. Int J Biol Sci 7:1037-44
Harland, Richard M; Grainger, Robert M (2011) Xenopus research: metamorphosed by genetics and genomics. Trends Genet 27:507-15
Hellsten, Uffe; Harland, Richard M; Gilchrist, Michael J et al. (2010) The genome of the Western clawed frog Xenopus tropicalis. Science 328:633-6
Jiang, Zhihua; Rokhsar, Daniel S; Harland, Richard M (2009) Old can be new again: HAPPY whole genome sequencing, mapping and assembly. Int J Biol Sci 5:298-303