Joint Genome Institute

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The Joint Genome Institute Production Genomics Facility is located in Walnut Creek, California.

The DOE Joint Genome Institute (JGI) was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore National Laboratory (LLNL), and Los Alamos National Laboratory (LANL). In 1999, the University of California, which managed the three national labs for the DOE, leased 60,000 square feet of laboratory and office space in a light industrial park in Walnut Creek, California, to consolidate activities and accommodate JGI's 160 employees in what is known now as the Production Genomics Facility (PGF). The JGI, led by Eddy Rubin, M.D., Ph.D., receives its funding from the Office of Biological and Environmental Research in DOE's Office of Science. Sixty percent of JGI sequencing is for the Community Sequencing Program (CSP), and the remaining 40% is for DOE programs. The vast majority of sequencing as part of these programs is related to the DOE mission areas of bioremediation, bioenergy, and carbon sequestration.

The JGI makes high-quality genome sequencing data freely available to the greater scientific community through its web portal. Having played a significant role in the federally funded Human Genome Project--generating the complete sequences of Chromosomes 5, 16, and 19--the JGI has now moved on to contributing in other critical areas of genomics research. While National Institute of Health-funded genome sequencing activities continue to emphasize human biomedical targets and applications, the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the science mission of the Department of Energy. With efficiencies of scale established at the PGF, and capacity now exceeding three billion bases generated on a monthly basis, the JGI has tackled scores of additional genomes. These include more than 60 microbial genomes and many important multicellular organisms and communities of microbes. In partnership with other federal institutions and universities, the JGI is in the process of sequencing a frog (Xenopus tropicalis), a green alga (Chlamydomonas reinhardtii), a diatom (Thalassiosira pseudonana) , the cottonwood tree (Populus trichocarpa), and a host of agriculturally important plants and plant pathogens. Microorganisms, for example those that thrive under extreme conditions such as high acidity, radiation, and metal contamination, are of particular interest to the DOE and JGI. Investigations by JGI and its partners are shedding light on the cellular machinery of microbes and how they can be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere, and produce potentially important sources of energy such as hydrogen and methane.

At the PGF, the JGI also supports programs dedicated to functional and evolutionary genomics related to the organisms and environments being sequenced and the development of computational and bioinformatic tools for data management and mining.

In February 2004, the JGI launched the Community Sequencing Program (CSP). The CSP was created to provide the scientific community at large with access to high-throughput sequencing at the JGI. Meritorious large-scale DNA sequencing projects are chosen based on outside scientific peer review. Through this program, the DOE has established the JGI as a user facility that will advance genomics research in a broad range of disciplines where DNA sequence information is likely to drive scientific discoveries.

In 2005, a Memorandum of Understanding (MOU) governing the operations of JGI was signed by the Directors of the original partner laboratories, LANL, LLNL, and LBNL, and two additional DOE National Laboratories, Oak Ridge National Laboratory (ORNL) and Pacific Northwest National Laboratory (PNNL). This MOU calls for the JGI, with the participation of these partnering DOE National Laboratories, to continue to apply large-scale sequencing and analysis to issues relevant to the DOE’s science mission.

The JGI is also home of the Integrated Microbial Genomes System (IMG) which provides a framework for comparative analysis of the genomes sequenced by the Joint Genome Institute. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective.