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African frog jumps ahead: Xenopus tropicalis to be sequenced


An African frog with small claws on its toes has leaped into the circle of animals whose genomes are being sequenced. By decoding the frog genome and comparing it to the human sequence, scientists hope to find new clues to how human genes function and how vertebrates evolve.

The African clawed frog Xenopus laevis (left) and its close relative, the smaller Xenopus tropicalis (right).

The tiny, fast-growing Xenopus tropicalis was selected over other frogs because it has one of the smallest genomes among amphibians. But it was not only the genome size that persuaded scientists at the US Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, California, to initiate the X. tropicalis Genome Project.

Frogs have been the subjects of laboratory research for decades, mostly in the field of early embryo development and cell biology. Frog embryos are relatively large and numerous, and they develop externally, which makes them easier to use for molecular and surgical experiments.

One species of Xenopus in particular—the African clawed frog Xenopus laevis—is considered the equivalent of the lab rat for amphibian studies. This larger cousin of X. tropicalis is popular with developmental biologists because X. laevis can be induced to ovulate and mate any time of the year. Most frog species are seasonal breeders.

The popularity of X. laevis grew when scientists discovered that the females lay eggs when exposed to a human hormone present in the urine of pregnant women. In the 1950s, X. laevis was commonly used in human pregnancy tests.

Despite its popularity among biologists, X. laevis wasn't selected for sequencing. Instead, JGI decided to sequence X. tropicalis, which shares most of the characteristics of its larger relative but has a much shorter generation time—four to six months. By comparison, it takes up to two years for X. laevis to reach maturity.

Another advantage of X. tropicalis is its small genome—about 1,700 million base pairs, or roughly half the size of its larger relative. Also, X. tropicalis has fewer chromosomes and the only diploid genome among the 14 Xenopus species. This means it has no more than two copies of most genes, whereas the other species of Xenopus have four copies of most genes (pseudotetraploid).

Molecular biologist Paul Richardson is leading the X. tropicalis project at JGI. At the annual Xenopus meeting this month in Cambridge, England, Richardson announced that the goal of the project is to produce a high-quality sequence and annotation that meets the needs of a large and diverse research community.

The name 'Xenopus' means 'strange foot.' Members of the Xenopus family have long fingers and webbed feet with small claws on three toes. They live in the water and swim. Frog lovers say that Xenopus make great pets because they are easy to take care of in an aquarium. But, they warn, keep a lid on the aquarium because they are also excellent jumpers.

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Joint Genome Institute to sequence key African frog genome. Press release, US Department of Energy's Joint Genome Institute (JGI), Walnut Creek, California (August 20, 2002).

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