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Pufferfish genome reveals nearly a thousand potentially new human genes


The Japanese pufferfish is not only a specialty in sushi restaurants, but also a valuable model for scientists fishing for genes in the human genome.

Researchers in Singapore, the U.K. and the U.S. have now published a draft genome sequence of Fugu rubripes—the fish with the smallest genome of any vertebrate known. Their comparison of the pufferfish and human genomes revealed nearly a thousand putative new human genes. These 961 human DNA sequences match Fugu genes and have so far not been reported in public gene databases.

Nearly 1,000 genes in the pufferfish Fugu rubripes are apparently identical to previously unidentified ones in humans.

Even though men and fish diverged from their common ancestor over 450 million years ago, the Fugu genome contains roughly the same number of genes as its human counterpart, which is eight times larger. The difference in size between the species is due to much more repetitive DNA in the human genome.

Three quarters of the pufferfish's 31,000 genes have direct human counterparts, including many that are involved in vertebrate anatomy and physiology, according to the study by the International Fugu Genome Consortium published online in Science.

Despite these similarities, it is the differences between the species that is generating much of the excitement about the new research. Among the 25 percent of human genes without counterparts in Fugu are key genes involved in the human immune system and metabolic regulation.

The pufferfish used in the study is also known as "torafugu"—a prized delicacy in Japanese cuisine, though potentially deadly if the organs that contain toxins are not properly removed.

Research by the International Fugu Genome Consortium to analyze the Fugu genome is ongoing. "My lab is concentrating on using Fugu and other completed vertebrate genome sequences to screen for functional regulatory elements in mammalian genomes," says Samuel Aparicio, of the University of Cambridge's Department of Oncology in the U.K., and a member of the research team.

The Fugu project was initiated 1989 in Cambridge, U.K., by a small research group led by molecular biologist Sydney Brenner, now at The Salk Institute in San Diego. In 2000, when it became clear that the compact pufferfish genome would help researchers find and analyze genes and regulatory elements in the human genome, the International Fugu Genome Consortium was formed.

Members of the Fugu consortium include Singapore's Institute of Molecular and Cell Biology (IMCB), the Joint Genome Institute (JGI) of the US Department of Energy in Walnut Creek, California, the UK Medical Research Council's Human Genome Mapping Resource Centre in Cambridge, and the American Institute for Systems Biology (ISB) in Seattle. Further collaborators are the University of Cambridge's Department of Oncology in the U.K., Celera Genomics in Rockville, Maryland, and Myriad Genetics in Utah.

The Fugu genome sequence and more information on the project can be accessed at

See related GNN articles
»A lean model genome: The Japanese pufferfish is sequenced
»The pufferfish: Clues to the human genome puzzle

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Aparicio, S. et al. Whole genome shotgun assembly and analysis of Fugu rubripes. Science Express. Published online July 25, 2002.

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