Issue 4 Summer 2002 - Applied Biosystems

8
technical communications
A Sequence to Die For!
Fugu Genome Draft Announced
by Michael D. O'Neill, BioBeat ® Online Magazine (www.biobeat.com)
O
n October 26, 2001, at the Genome Sequencing and
Analysis Conference (GSAC) in San Diego, California,
an international team of investigators, including
legendary molecular biologist Dr. Sydney Brenner,
announced completion of a draft sequence of the Fugu
rubripes genome.*
Dr. Sydney Brenner at the Gordon Conference on Human Molecular
Genetics in Newport, Rhode Island, August 1999.
(Photo by Michael D. O'Neill, BioBeat Online Magazine).
Fugu, a pufferfish, is a delicacy in Japan, but it can be a risky
meal, as it contains a deadly neurotoxin, and if not properly
prepared, can prove fatal to the diner. The Fugu genome is
particularly interesting to scientists because it contains very little
of the so-called ‘junk’ DNA that lies between gene segments in
other vertebrate genomes, particularly the human genome.
The Fugu genome is made up almost exclusively of
coding sequence, i.e., DNA that codes for proteins, and of
controlling regions that influence the expression of genes.
Consequently, study of the Fugu genome offers investigators a
potentially more direct route to the identification of genes and
the analysis of gene function, by allowing them to avoid the
complications of sifting through all the non-coding sequence
that is generally present in the genomes of higher organisms.
The Fugu genome is the smallest known vertebrate genome
(350-400 million DNA base pairs), but it is believed to contain
approximately the same number of genes as the much larger
human genome (3,000 million DNA base pairs) i.e., the Fugu
genome is more than eight times as gene-dense as the human
genome. In addition, the Fugu and the human genomes are
thought to share very similar sets of genes.
The porcupine fish (Cyclichthys orbicularis) belongs to a family (Diodontidae)
that is closely related to the pufferfish family (Tetraodontidae).
(Images courtesy of Jeff Jeffords, www.divegallery.com)
For these reasons, it is believed that sequence comparisons
between the Fugu genome and the human genome may
accelerate the identification of human genes, because genes
that can be relatively quickly identified in the gene-dense Fugu
genome can be used to find the corresponding genes in the much
less gene-dense human genome. Looking for a gene in the human
genome can be likened to looking for a needle in a haystack.
Looking for the corresponding gene in the Fugu genome may
allow the researchers to immediately eliminate a lot of the hay,
and thus simplify and accelerate the gene search.
A portion of the Fugu genome sequencing project was carried out
on ABI PRISM ® 3700 DNA Analyzers at Celera Genomics.
In addition, sequencing of cosmids from Fugu genomic libraries
was carried out at the Institute of Molecular and Cell Biology
(IMCB) in Singapore, which presently has two ABI PRISM 3700
DNA Analyzers and two ABI PRISM 377 DNA Sequencers.
Dr. Alice Tay, leader of the DNA Sequencing & Analysis Facility at the
Institute of Molecular and Cell Biology (IMCB) in Singapore.
(Image courtesy of Dr. Tay).
technical communications
IMCB Sequencing Leader Lauds Performance
of Applied Biosystems Sequencers
Dr. Alice Tay, leader of the DNA Sequencing & Analysis
Facility at the IMCB, said, “We are very pleased with the
performance of the DNA Sequencers from Applied Biosystems,
especially the quality of the data from the 3700 system.
Generally, the sequences are so clean that we are able to obtain
at least 500 bases for each read with almost no manual editing.”
Dr. Tay said the IMCB is presently focused on the finishing
phase of the Fugu genome sequencing project.
Additional information on the instruments used in this
sequencing project, as well as on other products from
Applied Biosystems, can be obtained in the Documents on
Demand section (http://docs.appliedbiosystems.com/search.taf)
of the Applied Biosystems web site: www.appliedbiosystems.com
Collaborating Institutions
The bulk of the Fugu genome sequencing project was carried
out at the United States Department of Energy’s Joint Genome
Institute (JGI). In addition to the JGI, Celera Genomics,
and the IMCB, other institutions collaborating on the Fugu
genome sequencing project included the Singapore Biomedical
Research Council, the Medical Research Council (UK),
the Cambridge University Department of Oncology, the Institute
for Systems Biology, and Myriad Genetics.
Annotated Version of Fugu Article Available in
Applied Biosystems’ Online Magazine
A web version of this article, with numerous links to
related information, is available in BioBeat Online Magazine
from Applied Biosystems. This online magazine can be accessed
at www.biobeat.com. BioBeat Online Magazine covers life
science research advances made around the globe and
presently includes over 120 richly annotated articles.
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*The original genus name for Fugu was Takifugu. The shorter name is now commonly used.
For more information on:
ABI PRISM family of DNA Analyzers enter: No. 405
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