Joint Genome Institute to sequence key African frog genome

DNA of Xenopus tropicalis will provide new clues to vertebrate development

In their continuing search for new clues to how human genes function and how vertebrates develop and evolve, researchers at the U.S. Department of Energy’s Joint Genome Institute (JGI) are gearing up to map the DNA of a diminutive, fast-growing African frog named Xenopus tropicalis.

Frogs have long been a favorite subject for biologists because their growth from eggs to tadpoles to mature organisms sheds light on the processes that guide the development of cells and organs. X. tropicalis was chosen for sequencing because its genetic structure is similar to humans but smaller and easier to decode than that of other frog species.

“Frogs and other amphibians occupy a key evolutionary position between mammals and fish, the organisms whose genomes have been or are currently being sequenced,” said Paul Richardson, the JGI project manager. “The publicly available Xenopus genome sequence will be a scientifically valuable resource for the research community.”

“Until now, experiments with frogs have shown us how vertebrates develop from an egg to an organism,” said Richard Harland, a developmental biologist at the University of California, Berkeley, and an early advocate of the project. “But we’re looking forward to new possibilities from the genome sequence.

“Using a compare-and-contrast approach with the human sequence, and the experiments that are possible in frogs, we’ll definitely make real progress in decoding the human genome,” Harland said.

Added Robert Grainger, a leading Xenopus researcher from the University of Virginia: “Studies on frogs have long been instrumental in understanding such fundamental processes as cell division and how cells in the embryo communicate with one another. Because these are the processes that go awry when birth defects occur or cancer strikes, we must seek a better understanding of them. This genome project will provide a major step in that direction.”

The JGI, one of the largest public genome sequencing centers in the world, is operated jointly by three DOE national laboratories managed by the University of California – Lawrence Berkeley and Lawrence Livermore in California, and Los Alamos in New Mexico. In addition to the Xenopus project, the JGI has genomics programs focused on microbes, fungi, fish, and plants.

The Institute brings together the research capabilities of the national labs and helps to convene multi-national teams that undertake large-scale genomic projects. This collaborative approach was used recently to sequence the genome of the pufferfish Fugu rubripes. Researchers reported last month that by comparing the Fugu sequence with the results of the Human Genome Project, they were able to predict the presence of nearly 1,000 previously unidentified human genes.

For the Xenopus project, the JGI convened an advisory board to organize and disseminate information about the sequencing effort. Members include researchers from the National Institutes of Health (NIH), UC Berkeley, UC Irvine, the University of Virginia, the Institute for Systems Biology in Seattle, Children’s Hospital in Cincinnati, and the University of Calgary in Canada, as well as from the United Kingdom and Japan. Steven L. Klein, chair of a Xenopus working group at NIH’s National Institute of Child Health and Human Development, noted that his agency will provide additional resources to NIH-sponsored labs to add data for this collaborative genome project.

JGI is a leader in sequencing organisms of crucial interest to researchers around the world. For the Human Genome Project, JGI sequenced human chromosomes 5, 16, and 19, which together constitute 11 percent of the human genome. JGI sequenced mouse DNA related to human chromosome 19 to illuminate the molecular evolutionary history of the two species. JGI has also sequenced the environmentally important white rot fungus (Phanerochaete chrysosporium) and nearly 50 important microorganisms.

With its main headquarters and Production Genomics Facility in Walnut Creek, JGI employs about 240 people and has programs in genomic sequencing, computation, functional genomics, genomic diversity, and new technology development. Funding is provided predominantly by the Department of Energy’s Office of Science, Office of Biological and Environmental Research. Other agencies that have contributed to funding JGI include DOE’s National Nuclear Security Administration, NIH, the National Science Foundation, and the U.S. Department of Agriculture.

Additional information and progress reports on JGI projects, including daily updates of sequence information and assembly statistics, are available at www.jgi.doe.gov. Xenopus annotation workshops for members of the research community will be held at the JGI’s facility in Walnut Creek.