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A lean model genome: The Japanese pufferfish is sequenced
By Birgit Reinert

An international consortium has completed the draft sequence of the Japanese pufferfish—the smallest known genome among vertebrates. Fugu rubripes and humans have a similar repertoire of genes, but Fugu has substantially less repetitive—or 'junk'—DNA. It is the first public assembly of a vertebrate species using the whole genome shotgun approach without any physical or genetic map.

The Japanese pufferfish Fugu rubripes.

Despite the difference in size—with about 365 million base pairs, Fugu is almost eight times smaller than the human genome—both Fugu and human have essentially the same genes and regulatory sequences. Current figures for Fugu are around 35,00 to 40,000 genes. With far less repetitive DNA to sort through, the fish genome will make it easier to identify sequences—and hence genes—in the human genome.

Comparing the sequence data of Fugu and human is expected to shed light on the underlying similarities and essential differences between the species. The genomes of Fugu and human separated hundreds of millions of years ago, and the similar sequences found between the two are believed to be essential for life.

The toxic saltwater fish is one of the world's deadliest delicacies. It is a popular food in Japan even though it can be lethally poisonous if prepared improperly. When eaten, the meat is reported to produce a pleasant, warm tingling. There are nearly 100 kinds of pufferfish worldwide. The puffer inflates—hence the name—when it considers itself in danger.

The completion of the Fugu sequencing project was announced at the 13th International Genome Sequencing and Analysis Conference (GSAC) in San Diego, California on October 26, 2001. The consortium intends to publish an analysis of the Fugu genome early in 2002.

Sydney Brenner, of The Salk Institute for Biological Studies in San Diego, California led the sequencing project. Members of the consortium include the US Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, California, the Institute for Molecular and Cell Biology (IMCB) in Singapore, and the MRC UK Human Genome Mapping Resource Centre (HGMP-RC), in Cambridge, England.

See related GNN articles
»A reference for the human genome: The Tetraodon pufferfish sequence
»The pufferfish: Clues to the human genome puzzle

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Elgar, G. et al. Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Gen Res 9, 960-971 (October 1999).
Brenner S. et al. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366, 265-268 (November 18, 1993).

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