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Fugu fish sequencing project potential boon to gene hunters

the JGI in this collaborative effort to sequence the Fugu genome are the Institute for Molecular and Cell Biology (IMCB) which is in Singapore and is led by Chris Tan; the MRC UK HGMP Resource Centre, which is in Cambridge and whose role in the sequencing of the Fugu genome will be led by Greg Elgar; The Molecular Sciences Institute, which is located in Berkeley and is led by Sydney Brenner who is also a Visiting Investigator at the IMCB; and the Institute for Systems Biology, which is located in Seattle and led by Lee Hood.

Evolution has conserved many of the DNA sequences used in genes to code for proteins or in the elements that regulate gene expression. This makes comparisons of genome sequences between species an effective and efficient means of finding new genes. Currently, the favorite genome models for gene hunters include those of the mouse, fruit fly, yeast, and nematode. Fugu is a wildly popular food in Japan even though it can be lethally poisonous if prepared improperly. The genome of this fish, with its 8-fold compactness compared to the human genome, should make it a very cost-effective model.

Explains Daniel Rokhsar, JGI's associate director for computational genomics, "Within each taxonomic grouping, there can be wide variations in genome size that are not necessarily related to the complexity of the organism. These variations appear to be due to differing amounts of 'junk' or 'selfish' DNA, often dominated by the remains of ancient viral-like genomic infections that left hundreds of thousands of repetitive elements littered throughout the genome. The Fugu genome seems to have avoided these events and sequencing it will therefore allow us to obtain a complete vertebrate genome extremely rapidly."

Under the terms of the consortium's agreement, the JGI will be responsible for both the production of draft sequences as well the computational aspects of the project. The Fugu genome will be sequenced following the same "shotgu
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Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
25-Oct-2000


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