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JGI Forms Consortium to Sequence Puffer Fish to Aid Comparative Genomic Analysis

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THE JOINT GENOME INSTITUTE of the US Department of Energy announced Thursday the formation of an international consortium to sequence Fugu rubripes, the potentially deadly Japanese delicacy known as the puffer fish.

Under the terms of the agreement, JGI will produce the draft sequences as well as determine the computational aspects of the project. Daniel Rokhsar, JGI’s associate director for computational genomics, is currently overseeing the development of customized software for the project.

Trevor Hawkins, deputy director of the JGI, said that the software developers were seeking to create a whole genome assembly engine that could accommodate the Fugu’s relatively large size.

“Those [tools] that exist right now are being used for assembly of BACs and smaller microbes that are not as big as the Fugu,” Hawkins said. “They don’t use such things as paired-end reads.”

JGI scientists anticipate having more than 95 percent of the Fugu genome sequence available in an accessible database by March 2001. They will use the shotgun strategy for sequencing the genome, which the JGI also used to complete the draft sequences of human chromosomes 5, 16, and 19.

Hawkins said the consortium would begin the sequencing phase on November 1. He said the project would likely spend between $7 million and $10 million on this phase alone.

The consortium’s long-term goal is to generate complete sequence coverage of the Fugu genome and assemble it into a finished form for comparative genomic analysis. The project is also planning to build tools for three-way comparisons between the genomes of the mouse, human, and Fugu.

Researchers believe that the sequenced Fugu genome will offer great insights into understanding the human genome. The Fugu genome contains essentially the same genes and regulatory sequences as the human genome. However, the Fugu genome consists of approximately 400 million bases as compared to the 3 billion bases in humans. This means the Fugu contains much less junk DNA, making it easier to identify genes.

The other members of the consortium, namely Singapore’s Institute for Molecular and Cell Biology, the MRC UK HGMP Resource Center in Cambridge, UK, the Molecular Sciences Institute in Berkeley, and Leroy Hood’s Institute for Systems Biology in Seattle, will be responsible for the finishing phase of the project as well as contributing to the computational analysis of the genomic data.

Nobel laureate James Watson applauded the project. “The Fugu fish sequence, in combination with the draft mouse genome, to be available in early 2001, will greatly add to the comparative sequence studies that are now required to isolate coding and non-coding conserved elements within the human genome,” Watson said in a statement.

Hawkins said that the project would represent the institute’s largest genome sequencing project to date. It will also form the centerpiece of the JGI’s new genome portal, he said. This portal, which is currently being developed, can be accessed at www.jgi.doe.gov. The website, which will eventually contain all of the JGI’s software tools as well as information about news and events, is scheduled to be completed by January.

—Jennifer Friedlin

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