Researchers at the HudsonAlpha Institute for Biotechnology, in collaboration with a group of scientists affiliated with 46 institutions around the world, have sequenced an African clawed frog genome and used it to better understand the evolutionary history of the clawed frog. Their research was published today in Nature.

“The most exciting finding in our analysis of the genome of Xenopus laevis is that we could find distinct transposable element relicts that proved the whole-genome duplication to be the result of two extinct progenitor species,” said Adam Session, PhD. “While this has been shown in many grasses, this is the first time this has been experimentally shown without extant progenitors.” Session is a lead author of the paper and a researcher at the Department of Energy Joint Genome Institute.

For its role in the project, the HudsonAlpha Genome Sequencing Center (GSC) contributed to the sequencing and improvement of the Xenopus laevis genome, commonly called the African clawed frog. The sequencing at HudsonAlpha was led by Jeremy Schmutz and Jane Grimwood, PhD, both faculty investigators and co-directors of the center, and Jerry Jenkins, PhD, genome analysis group leader in the GSC. Schmutz is also the plant program lead at the Department of Energy Joint Genome Institute.

The African clawed frog has a complex tetraploid genome. Humans have a diploid genome, meaning each person’s cells usually contain a pair of chromosomes – one from each biological parent. Tetraploid genomes have four pairs of chromosomes, which is fairly common in plants but rare in animals.

The clawed frog genome is important for scientific research because the amphibian is often used as a model to discover the molecular mechanisms fundamental to life, providing a shortcut to understanding human biology.

“Xenopus has become a major vertebrate model supporting cellular and developmental biology research important to major drivers of medical research like the National Institutes of Health,” said GSC co-director Schmutz. “We are pleased to continue to provide high-quality genome sequencing that can be used for new discoveries in the scientific community.”

Once the X. laevis genome was sequenced, researchers in the United States and Japan compared that newly sequenced genome to a related frog genome, X. tropicalis, commonly called the Western clawed frog. In contrast to the tetraploid African clawed frog, the Western clawed frog has a diploid genome.

The GSC also sequenced the X. tropicalis genome, which was published in Science in 2010.

“While we typically work on plant genomes, this was a fantastic opportunity to continue our work with the Xenopus project,” said Jenkins, the genome analysis group leader. “We’re excited about what was learned from comparing the two genomes.”

With the two genomes sequenced, the team of scientists was able to take a closer look at the evolutionary relationship between the two frogs. The paper in Nature describes how two now-extinct frog species, each with a diploid genome, combined about 17 million years ago to form a frog with a tetraploid genome.

“With current funding from NIH, we are continuing to improve the completeness and accuracy of these two paired frog genomes in order to enable functional genomics with these developmental models,” said Jane Grimwood, PhD.

The Nature paper was authored by 74 scientists affiliated with institutions in seven countries.

Photo: The newly sequenced genome of X. laevis (on top) is compared to the X. tropicalis (two frogs on bottom) genome to understand evolution of clawed frogs in a Nature paper published this week. Image credit: Atsushi Suzuki, PhD, of the Institute for Amphibian Biology, at Hiroshima University in Japan.