JGI-Led Team Sequences Frog Genome

A team of researchers led by investigators at the Department of Energy's Joint Genome Institute reported online today in Science that they have sequenced the first amphibian genome: that of the Western clawed frog Xenopus tropicalis.

The international research team used shotgun sequencing to generate a draft version of the X. tropicalis genome, which they then compared with the human and chicken genomes. In the process, they found more than 20,000 protein-coding genes in the frog genome, as well as regions of synteny with humans and chickens, and a slew of transposable element sequences.

And because amphibians diverged from the amniote lineage leading to mammals, birds, and reptiles some 360 million years ago, senior author Daniel Rokhsar, a researcher affiliated with JGI and the University of California at Berkeley, and his co-authors explained, information in the X. tropicalis genome is helping to reconstruct features found in the shared ancestor of these animals and uncovering clues about vertebrate evolution in general.

The African clawed frog X. laevis is commonly used as a laboratory model for studying everything from cell biology to vertebrate embryonic development. But genetic studies of X. laevis have been complicated by the frog's large, duplicated genome.

To bypass this problem, the team decided to first tackle the genome of a related frog species, X. tropicalis, which has a diploid genome that's roughly half the size of the X. laevis genome.

"It will be tremendous to have a high quality sequence of X. tropicalis upon which to build the X. laevis sequence," co-author Richard Harland, a researcher with UC Berkeley's Center for Integrative Genomics, said in a statement.

The team used shotgun sequencing to sequence the roughly 1.7 billion base genome of a female frog from a Nigerian, X. tropicalis inbred line, generating sequence that covered the genome about 7.6 times.

Their subsequent analysis of the genome turned up between 20,000 and 21,000 protein-coding genes. Around 1,700 of these appear to be orthologs of genes previously implicated in human disease, representing some 79 percent of known disease genes.

Among the gene families that appear to be expanded in the genome are an olfactory receptor family found specifically in tetrapods, a protocadherin family, and pheremone and bitter taste receptor families.

The X. tropicalis genome also contained large stretches of synteny with both human and chicken chromosomes, which the team used to help pin down lineage specific fusions and breakpoints.

The researchers used this synteny — along with markers from the frog's genetic map — to arrange scaffolds on the frog's linkage map.

Comparisons between the frog, human, and chicken genomes also provided new clues about amniote and vertebrate evolution. For example, the team estimated that human chromosomes harbor around 22 fusion events and 21 breakage events — far more than the four fusions and single break identified in the chicken genome.

And the researchers concluded that the amniote ancestor likely had 23 or 24 chromosomes — about double the number of chromosomes thought to have existed in vertebrate and eumetazoan ancestors.

"Both the vertebrate and eumetazoan ancestors have been suggested to have had about a dozen large chromosomes," they wrote. "The current analysis indicates that the amniote ancestor had twice as many, suggesting substantial chromosome breakage on the amniotic stem."

The frog genome is also replete with transposable elements, which made up more than a third of the genome sequence, the researchers noted. But whereas most other vertebrate genomes assessed so far contain mainly retrotransposons, nearly three-quarters of the transposable elements in the frog genome are DNA transposons.

Along with its potential for improving researchers' understanding of evolutionary biology, the genome sequence is already providing information about specific processes previously studied in Xenopus, including development and immune system function.

In addition, those involved in the study highlighted the usefulness of the X. tropicalis genome for genetically characterizing the more complex and commonly used model organism X. laevis. Some members of the X. tropicalis genome sequencing team have reportedly applied for a National Institutes of Health grant to facilitate sequencing of the X. laevis genome.

"Given the utility of the frog as a genetic and developmental biology system and the large and increasing amounts of cDNA sequence from the pseudo-tetrapoloid X. laevis, the X. tropicalis reference sequence is well poised to advance our understanding of genome and proteome evolution in general, and vertebrate evolution in particular," the researchers concluded.