News of the WeekGenomics

Frog DNA Yields Clues to Vertebrate Genome Evolution

Science  30 Apr 2010:
Vol. 328, Issue 5978, pp. 555
DOI: 10.1126/science.328.5978.555

Add another group of animals to the growing menagerie of creatures whose genomes have been sequenced. On page 633 of this issue, Uffe Hellsten, a bioinformaticist at Lawrence Berkeley National Laboratory in California, and his colleagues describe the sequence of the Western clawed frog, Xenopus tropicalis, the first member of the amphibian branch of the tree of life to be so honored.

Amphibians branched off from other vertebrates about 350 million years ago, and the group has been evolving along a path separate from mammals, reptiles, and birds ever since. “For this reason, the frog genome sequence provides unique insights into genome dynamics over an extended period of evolution,” says Ben Evans of McMaster University in Hamilton, Canada. “It fills in a crucial gap in our understanding of genome diversity and evolution of organisms,” adds David Cannatella, an evolutionary biologist at the University of Texas, Austin.

Floating to fame.

An aquatic frog, the Western clawed frog, now has a sequenced genome.

CREDIT: DAVID CANNATELLA/UNIVERSITY OF TEXAS

The draft of the genome is in hundreds of pieces—not complete enough to be ordered chromosome by chromosome, but Hellsten and colleagues were able to match long stretches of contiguous sequence with equivalent sequences in the chicken and human genomes. A 150-million-base region in the center of human chromosome 1, for example, has a virtually identical counterpart in the frog and chicken genomes. “That implies that whole region has remained intact for 350 million years,” says Hellsten, and it represents an ancient chromosome. Other matchups indicated that three stretches of DNA fused onto human chromosome 1 after breaking off from elsewhere in the genome. Another intact region in chicken and frog split up in the human genome and spread across six chromosomes. “There appears to have been more frequent chromosome fusion and fission in mammals than in birds and frogs,” says Evans.

The frog genome may offer new insights for not only evolutionary biologists but also biomedical scientists. It has 1700 genes that have been linked to human diseases such as type 2 diabetes, acute myeloid leukemia, alcoholism, sudden infant death syndrome, and congenital muscular dystrophy. These can be investigated using the frog to probe the basic mechanisms by which these genes work. “It opens a large number of doors for comparative and functional genomics,” says Erica Bree Rosenblum, an evolutionary biologist at the University of Idaho, Moscow.

Researchers chose X. tropicalis to be the first amphibian sequenced because developmental biologists use it in their studies and it has a relatively small genome: 1.7 billion bases stretched across 10 chromosomes, about half the size of the human genome. Now, researchers are hungry for more. “One species of frog does not allow one to say very much about frogs,” says Cannatella. Others point out that Xenopus is unusual among frogs, so “now they need to do a typical frog,” says David Wake, an evolutionary biologist at the University of California, Berkeley. Cannatella would like to see the fire-bellied toad, Bombina orientalis, sequenced next.

Nonetheless, says Stephen O'Brien, a geneticist at the National Cancer Institute branch in Frederick, Maryland, this Xenopus genome “is an important beginning and a treat for comparative genomics.”

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