An international research consortium led by the U.S. Department of Energy’s Joint Genome Institute (JGI) reported today on the draft sequencing, assembly, and analysis of the genome of the Japanese pufferfish Fugu rubripes. The report was released on Science Magazine’s Science Express Web site.
Pufferfish have the smallest known genomes among vertebrates, the group of animals with backbones that includes humans. The Fugu sequence contains roughly the same number of genes as the much larger human genome, but in a compact form streamlined by the relative scarcity of the “junk” DNA that fills much of the human sequence.
Through comparison of the human and pufferfish genomes, the researchers were able to predict the existence of nearly 1,000 previously unidentified human genes. These additional hypothetical human genes are of largely unknown function, but contribute to the complete catalog of human genes. Determining the existence and location of genes helps enable scientists to begin characterizing how they are regulated and function in the human body.
“Comparative genomics programs like the Fugu project are key to understanding the biology of the human genome,” said JGI Interim Director Eddy Rubin. “As historic and important as the Human Genome Project is, it’s only the first step in determining how genes work–and why they sometimes don’t work the way they should.”
The draft sequencing and assembly of the Fugu genome, announced last October, marked the first publicly released animal genome after the human sequence, and the first vertebrate genome publicly sequenced and assembled using the whole genome shotgun method. The Fugu genome sequence, along with other information about the project, is available on the World Wide Web at genome.jgi.doe.gov/fugu.
The JGI, one of the largest public genome sequencing centers in the world, is operated jointly by three DOE national laboratories managed by the University of California–Lawrence Berkeley and Lawrence Livermore in California, and Los Alamos in New Mexico. In addition to the Fugu project, the JGI has genomics programs focused on microbes, fungi, animals, and plants.
Fugu is a delicacy in Japanese cuisine that can deliver a deadly neurotoxin if improperly prepared. Its scientific value, however, is based on its small genome size. According to Daniel Rokhsar, Associate Director for Computational Genomics at the JGI, the compact structure of the Fugu genome (only one-eighth the size of its human counterpart) made it possible to identify genes that had been obscured by the many repetitive and non-coding sequences that make up about 97 percent of human DNA.
Rokhsar noted that nearly three-fourths of the genes in the human genome have identifiable counterparts in Fugu, highlighting the shared anatomy and physiology common to all vertebrates. “These similarities are recognizable in the two genome sequences despite the 400 million years of evolution since the two species diverged from their common ancestor,” he said. “Proteins found in humans but not in pufferfish, and vice versa, help define the sets of genes at the core of differences between four-limbed animals (reptiles, amphibians, birds, and mammals, including humans) and finned fish.”
“For the first time we are seeing the overall differences as well as the similarities in the protein parts that make up fish and man,” said Dr. Samuel Aparicio, Principal Investigator at the Wellcome Trust Centre for Molecular Mechanisms in Disease at the Department of Oncology, Cambridge University, England. “When we matched the predicted Fugu proteins directly against the human genome sequence, for 961 cases we found that there was a match in human which didn’t overlap an already predicted or known human gene.
“This flags up for human geneticists the position of potentially novel human genes in the human genome,” Aparicio said. “In addition, direct comparisons of the fish DNA with the human DNA show that more human genes will be found by comparing fish with man. In this way, the pufferfish sequence is helping to find previously undiscovered features in the human genome sequence–a process often compared to the decipherment of the Rosetta stone.”
The study also revealed how the ordering of genes in genomes can be shuffled over time. Many small groups of genes are found in the same order in man and fish, but over longer distances the ordering of genes becomes scrambled. The rearrangements found by the researchers shed light on the processes that drive genome evolution.
The International Fugu Genome Consortium was formed in November 2000 by the JGI and the Singapore Biomedical Research Council’s Institute for Molecular and Cell Biology. Other members of the consortium are the UK Medical Research Council’s Human Genome Mapping Resource Centre in Cambridge, England, the Cambridge University Department of Oncology, and the Institute for Systems Biology in Seattle, Washington. Contributing to the consortium’s sequencing efforts were two U.S. companies, Celera Genomics of Rockville, MD and Myriad Genetics, Inc., of Salt Lake City, UT.
JGI is a leader in sequencing organisms of crucial interest to researchers around the world. For the Human Genome Project, JGI sequenced human chromosomes 5, 16, and 19, which together constitute 11 percent of the human genome. JGI sequenced mouse DNA related to human chromosome 19 to illuminate the molecular evolutionary history of the two species. JGI has also sequenced the environmentally important white rot fungus (Phanerochaete chrysosporium) and nearly 50 important microorganisms.
With its main headquarters and Production Genomics Facility in Walnut Creek, JGI employs about 240 people and has programs in genomic sequencing, computation, functional genomics, genomic diversity, and new technology development. Funding is provided predominantly by the Department of Energy Office of Science’s Biological and Environmental Research Program. Other agencies that have contributed to funding JGI include DOE’s National Nuclear Security Administration, the National Institutes of Health, the National Science Foundation, and the U.S. Department of Agriculture