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The Fugu Genome
An Uncommon Sensor
Microbial Marathon
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This issue...
News in Brief
View from the Inside
The Fugu Genome
An Uncommon Sensor
Microbial Marathon
People
About
Subscribe Free
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Fuguthe Poisonous Pufferfish:
New Genome Model for Gene Hunters
by Paul Preuss
The Fugu fish (Fugu rubripes) is a wildly popular food in Japan even though it can be lethally poisonous if prepared improperly. This Japanese delicacy, also known as the pufferfish or blowfish, will soon become more than just a risky mouthful. The Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE) has chosen the Fugu as its next genome sequencing project. JGI will lead an international consortium of researchers in a collaborative effort to sequence the genome of the Fugu.
The Japanese harvest the Fugu for consumption and export. There are over 1,500 fugu restaurants in Tokyo, where an average of 100-200 people a year show signs of poisoning, and the death rate is 61%. The liver and ovaries of the fish contain a potent neurotoxin called tetrodotoxin (TTX).
The Fugu genome was chosen because it contains essentially the same genes and regulatory sequences as the human genome, but it carries those genes and regulatory sequences in approximately only 400 million bases as compared to the 3 billion bases that make up human DNA. With far less so-called "junk DNA" to sort through, finding genes and controlling sequences in the Fugu genome should be a much easier task. The information can then be used to help identify these same elements in the human genome.
JGI's associate director for computational genomics Daniel Rokhsar explains, "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."
Comparisons of genome sequences between species is an effective means of finding new genes because evolution has conserved many of the DNA sequences used in genes to code for proteins or in the elements that regulate gene expression. Currently, the favorite genome models for gene hunters include those of the mouse, fruit fly, yeast, and nematode. The genome of the Fugu fish, with its eight-fold compactness compared to the human genome, should make it a cost-effective model.
 
Fugu rubripes: The Fugu inflates his body to scare away enemies by gulping down water.
Said Energy Secretary Bill Richardson, "This genetic information from a distantly related vertebrate will help us read the book of human life with new understanding and knowledge. Given the major contributions already made to the human genome project by the Energy Department's Joint Genome Institute and their tremendous capability to decode DNA, this new effort is a logical and exciting next step in the project."
Based in Walnut Creek, California, the JGI is one of the largest publicly funded genome sequencing centers in the world. The institute is itself a consortium initially formed by three DOE national laboratories, Lawrence Berkeley, Lawrence Livermore, and Los Alamos.
Members of the JGI Fugu genome sequencing consortium include the Institute for Molecular and Cell Biology (IMCB) in Singapore, led by Chris Tan; the UK Human Genome Mapping Resource Centre in Cambridge, led by Greg Elgar; the Molecular Sciences Institute in Berkeley, California, led by Sydney Brenner who is also a visiting investigator at the IMCB; and the Institute for Systems Biology in Seattle, led by Lee Hood.
Under the terms of the consortium's agreement, the JGI will be responsible for both the production of draft sequences as well as the computational aspects of the project. The Fugu genome will be sequenced following the same "shotgun strategy" used so successfully by JGI researchers to complete the draft sequences of human chromosomes 5, 16 and 19. To speed the process even faster for the Fugu genome, researchers will use customized software now being developed at the JGI under the direction of Rokhsar. JGI scientists anticipate that more than 95-percent of the Fugu genome sequence will be available in an accessible database by March 2001.
The other members of the consortium will be responsible for the finishing phase of the project as well as contributing to the computational analysis of the genomic data. The long-term goal of this consortium is to generate complete sequence coverage of the Fugu genome and assemble it into a finished form for comparative genomic analysis.
Nobel laureate James Watson, co-discoverer of DNA's double helix structure, has endorsed this 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."
Sydney Brenner's pioneering studies of Fugu biology with Greg Elgar and his colleagues helped show that the organization of Fugu genes parallels that of human genes. Brenner said, "I am delighted that DOE has decided to sequence Fugu. The data will greatly enhance the identification of gene promoter regions and lead to a much better understanding of the human genome."
This research is supported through DOE's Office of Science.
Media contacts:
Dr. Trevor Hawkins, Joint Genome Institute, (925) 296-5682, e-mail: TLHawkins@lbl.gov
Dr. Chris Tan, Institute for Molecular and Cell Biology, Singapore, e-mail: yht@mcbsgs1.imcb.nus.edu.sg
Dr. Greg Elgar, UK Human Genome Mapping Resource Centre, e-mail: gelgar@hgmp.mrc.ac.uk
Dr. Lee Hood, Institute for Systems Biology, can be reached through Tawny Biddulph or Kevin Evanto at (206) 652-9506, e-mail: tbiddulph@systemsbiology.org
or e-mail: kevin@cofen.com
For more information:
DOE Joint Genome Institute, October 26, 2000 press release.
"Pufferfish: The Lean, Mean Genome," New Scientist, July 2000.
"The Pufferfish: Clues to the Human Genome," CeleraScience, June 23, 2000
"Pufferfish: Sushi or Science?" Wired, June 12,2000
"DNA Dilemma: Scientists Debate Which Creature's Genetic Code to Decipher Next," Seattle Post Intelligencer, December 28, 1999
Fishing for genes: Fugu expands (but its genome doesn't), by Greg Elgar, UK Human Genome Mapping Resource Centre.
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