Seeing double. The genome of the tiny puffer fish reveals that its ancestors duplicated their genome sometime after diverging from the lineage of humans and other vertebrates.

Puffed-Up Genome

When genomes were handed out, it appears that an ancient vertebrate upped the ante and went double or nothing. A newly published draft sequence of a puffer fish genome suggests that the vertebrate ancestor shared by bony fishes and humans had just 12 pairs of chromosomes, but the fishes doubled up after their lineage split from our own. The analysis gives scientists a peek at the past and promises to shed light on how genomes evolve.

The spotted green puffer fish Tetraodon nigroviridis is one of about 20,000 kinds of ray-finned fishes, a group characterized by small bones in their fins. About 450 million years ago, the ancestor of ray-finned fishes went on its own evolutionary tangent, splitting off from the vertebrate lineage that includes lobe-finned fishes, frogs, chickens, and humans. Studies of gene families in other ray-finned fishes hinted that at some time during the ray-finned evolution, the entire genome was duplicated (Science, 27 November 1998, p. 1711). But with limited evidence, the idea remained controversial.

Now efforts by scientists at the Massachusetts Institute of Technology and Harvard University in Cambridge and Genoscope in Evry Cedex, France, have put the controversy to rest. Led by evolutionary genomicist Olivier Jaillon of Genoscope, the researchers created a draft sequence of the puffer fish genome, the smallest known in vertebrates, and plotted the chromosome positions for hundreds of duplicated genes. On the puffer fish's 21 chromosomes they found several sections on different chromosomes that contained the same genes. When they compared the locations of more than 6000 puffer fish genes to the positions of related genes in the human genome, they discovered that one chromosomal region in humans matched to two regions in the puffer fish, across the entire genome. This suggests that the common ancestor of humans and puffer fish had only 12 chromosomes, and after the ray-finned fishes went their evolutionary way, the genome duplicated, the researchers report in the 20 October issue of Nature.The small size of the puffer fish genome suggests that there was a massive elimination of extra DNA following the duplication, says Hugues Roest Crollius, formerly of the Genoscope team. The draft genome will be a "tremendous resource," says Paramvir Dehal of the Joint Genome Institute in Walnut Creek, California, shedding light on how genomes and gene pathways evolve. It is already helping to answer questions about the evolution of our own genome, such as why we have far more gene rearrangements than the lowly puffer fish.

Related sites
Tetraodon Genome Browser
The ray-finned fishes from the University of California, Berkeley, Museum of Paleontology