DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

    More

    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

    More

    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

News & Publications
Home › News Releases › Pufferfish DNA Yields Clues to Human Biology

July 25, 2002

Pufferfish DNA Yields Clues to Human Biology

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

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

iPHoP: A Matchmaker for Phages and their Hosts

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.

New Research Sheds Light on Diversity in the Deep Sea

A photo taken in the deep sea. Black clouds billow out of hydrothermal vents.

Sequencing Sphagnum Leads to Discovery of Sex Chromosomes

A photo of two sphagnum species: S. divinum (red) and S. angustifolium (green)]

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.

Tracing the Evolution of Shiitake Mushrooms

A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California