NEW YORK, Oct. 25 — The US Department of Energy’s Joint Genome Institute and the Singapore Biomedical Research Council’s Institute for Molecular and Cell Biology announced today that they have completed a draft sequence of the fugu genome at a cost of about $10 million. Also known as the Japanese pufferfish, the organism is a delicacy of Japanese cuisine as well as a producer of a deadly neurotoxin.
The International Fugu Genome Consortium, formed in November of last year, chose to sequence fugu before more ordinary vertebrate experimental animals such as the zebrafish or the rat because its genome includes very little noncoding DNA. Although the fugu has approximately the same number of genes as the human genome, those genes are buried in only about 365 million base pairs of DNA.
“These fishes are somewhat unique in that they did not go through genomic duplications, so they have incredibly small genomes — eightfold smaller than humans,” said Trevor Hawkins, the director of the JGI and the leader of the international fugu genome research consortium.
“The fugu sequence is validating a lot of putative human genes, allowing us to find a lot of regulatory elements within the human genome,” he added. “We have a poor understanding of the exact structure of genes, and a very poor understanding of the regulatory switches that control the genes, and this is vital. It’s the next logical step.”
Hawkins said that another key feature of this sequence is that, unlike the mouse genome, it has been assembled. “It shows that we were able to perform whole genome shotgun using no mapping information,” he said. “The assembly is looking stunningly beautiful, a testimony that this approach works and is going to work for future genomes.”
The international fugu consortium, which had support from Celera Genomics and Myriad Genetics among others, is one of the largest international genome sequencing collaborations outside the human genome project.
The completion of the draft sequence is to be formally announced on Friday at the International Genome Sequencing and Analysis Conference in San Diego. Data from the project will then be available on the web.