Research on the amphibian Xenopus has provided numerous new insights into cell and developmental biology. With their large size and abundance, they provide unparalleled material for biochemical and cell biological analysis of complex processes such as the cell cycle and chromosome mechanics. For embryological experiments, the embryos are readily manipulated by microsurgery or microinjection, and can be subjected to both gain or loss of gene function. In order to make Xenopus more useful for the modern age of "systems biology" where proteomic and genomic analyses promise a comprehensive understanding of life's processes, we propose here to continue improvement of both the short range, and long range (chromosome level) assemblies of Xenopus tropicalis and Xenopus laevis. To achieve new insights into the function of both coding and non-coding DNA in the Xenopus clade, and add new information from outgroups, we will assemble the pseudotetraploid genomes of X. mulleri, X. epitropicalis, and X. borealis. These allotetraploid Xenopus species will provide new insights into the evolution of tetraploid genomes and aid in annotating non-coding sequences of Xenopus. In addition, we will assemble genomes for other outgroups, including the direct developing frog Eleutherodactylus coqui, the Tungara frog Engystomops, and the spadefoot toad, Spea, all of which are models for developmental, neurobiological or behavioral studies. These will also provide outgroup sequences for comparison and annotation, as well as enabling molecular approaches for the communities who study these frogs for their developmental or neurobiological advantages. We will provide genome assemblies and automated annotation of the comparative information to Xenbase and deposit gene and protein collections in public databases to ensure that the resources are widely available.

Public Health Relevance

Xenopus and other frogs have been crucial models to understand developmental and cell biology. Improved molecular resources and comparative genomics of frogs will provide new insights into gene function and regulation, and extend new systems biology approaches to novel questions in neurobiology, developmental biology and evolution, using the optimal amphibian species.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM086321-06
Application #
8719126
Study Section
Special Emphasis Panel (ZRG1-GGG-A (50))
Program Officer
Hoodbhoy, Tanya
Project Start
2009-01-01
Project End
2017-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
6
Fiscal Year
2014
Total Cost
$290,228
Indirect Cost
$100,228
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