Joint Genome Institute

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The Integrative Genomics Building (IGB) at Lawrence Berkeley National Laboratory (Berkeley Lab), the home of the DOE Joint Genome Institute and the DOE Systems Biology Knowledgebase (KBase). The Advanced Light Source (ALS) is above in the background. Glowing ALS-IGB XBD201906-00793012.jpg
The Integrative Genomics Building (IGB) at Lawrence Berkeley National Laboratory (Berkeley Lab), the home of the DOE Joint Genome Institute and the DOE Systems Biology Knowledgebase (KBase). The Advanced Light Source (ALS) is above in the background.

The Joint Genome Institute (JGI) is a scientific user facility for integrative genomic science at Lawrence Berkeley National Laboratory. [1] The mission of the JGI is to advance genomics research in support of the United States Department of Energy's (DOE) missions of energy and the environment. It is one of three national scientific user facilities supported by the Office of Biological and Environmental Research (BER) within the Department of Energy's Office of Research. [2] These BER facilities are part of a more extensive network of 28 national scientific user facilities that operate at the DOE national laboratories. [3] [4]

Contents

The JGI advances genomics research by providing the research community with access to the latest generation of genome sequencing and analysis capabilities. It employs a staff of 250 scientists, technicians, and other personnel to support the research of the 2,180 scientific users who make use of it for their research each year. [5] The facility sequenced 658 trillion total bases in FY 2022, and this output is now doubling about every two years. [6]

Research at JGI

Research at JGI is organized into seven programs: [7]

The JGI provides users with access, at no cost, to high-throughput genomic and specialized capabilities and data analysis. [8] Researchers submit proposals to one of the seven JGI user programs, and all proposals are reviewed for scientific merit and relevance to the DOE research mission. If the proposal is approved, the JGI provides the users a number of standard sequencing, synthesis, and metabolomics products.

Collaborations

The JGI collaborates extensively with the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory (PNNL). The two facilities jointly manage the Facilities Integrating Collaborations for User Science (FICUS) program, designed for researchers who require the capabilities of both user facilities to perform their research. The JGI also performs extensive sequencing on behalf of the four DOE Bioenergy Research Centers. [9] [10]

Leadership

The Director of JGI since 2017 is Nigel Mouncey. [11] Mouncey also serves as the President of the Society for Industrial Microbiology and Biotechnology (SIMB) [12]

History

The 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 (Berkeley Lab), Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL).In 1999, the University of California, which manages the three national labs for the DOE, leased laboratory and office space in a light industrial park in Walnut Creek, California to consolidate genome research activities. Led by biotechnology industry veteran Nigel Mouncey, who assumed the position of Director in March 2017, the DOE JGI receives its funding from the Office of Biological and Environmental Research in DOE's Office of Science.

Originally established to work on the Human Genome Project—the JGI generated the complete sequences of Chromosomes 5, 16 and 19—the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the DOE's science mission. Since 2004, the JGI has been a user facility that advances genomics research in a broad range of disciplines where DNA sequence information is likely to drive scientific discoveries. [13]

In February 2004, the JGI launched the Community Sequencing Program (CSP), known as the Community Science Program, which provides the scientific community at large with access to high-throughput, high-quality sequencing, DNA synthesis, metabolomics and analysis capabilities. The projects involve many important multicellular organisms, microbes and communities of microbes called metagenomes (or microbiomes) related to the DOE mission areas of bioenergy, understanding global cycles such as the carbon cycle, and biogeochemistry and are chosen primarily based on scientific merit as determined by outside review. [14]

Genome sequencing milestones

In 2006, the JGI published the genome of the first tree sequenced—the cottonwood (Populus trichocarpa). [15] In partnership with other federal institutions and universities, the JGI has also published the genome sequences of sorghum, a candidate feedstock for biofuels and biomanufacturing. [16]

Data management systems

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. These genome and metagenome/microbiome analysis systems include Genome Portal, Phytozome, IMG and the Genomes OnLine Database.

The Integrated Microbial Genomes System (IMG), which provides a framework for comparative analysis of primarily microbial genomes, though the system also supports eukaryotic genomes and environmental samples. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective.

Related Research Articles

<span class="mw-page-title-main">Genomics</span> Discipline in genetics

Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

<span class="mw-page-title-main">Lawrence Berkeley National Laboratory</span> National laboratory located near Berkeley, California, U.S.

Lawrence Berkeley National Laboratory (LBNL) is a federally funded research and development center in the hills of Berkeley, California, United States. Established in 1931 by the University of California (UC), the laboratory is sponsored by the United States Department of Energy and administered by the UC system. Ernest Lawrence, who won the Nobel prize for inventing the cyclotron, founded the Lab and served as its Director until his death in 1958. Located in the Berkeley Hills, the lab overlooks the campus of the University of California, Berkeley.

<span class="mw-page-title-main">United States Department of Energy National Laboratories</span> Laboratories owned by the United States Department of Energy

The United States Department of Energy National Laboratories and Technology Centers is a system of laboratories overseen by the United States Department of Energy (DOE) for scientific and technological research. The primary mission of the DOE national laboratories is to conduct research and development (R&D) addressing national priorities: energy and climate, the environment, national security, and health. Sixteen of the seventeen DOE national laboratories are federally funded research and development centers administered, managed, operated and staffed by private-sector organizations under management and operating (M&O) contracts with the DOE.

<span class="mw-page-title-main">J. Craig Venter Institute</span> Non-profit genomics research institute

The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research (TIGR), the Institute for Biological Energy Alternatives, and the J. Craig Venter Science Foundation Joint Technology Center. It has facilities in Rockville, Maryland and San Diego, California.

<span class="mw-page-title-main">Metagenomics</span> Study of genes found in the environment

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.

<span class="mw-page-title-main">Human Genome Project</span> Human genome sequencing programme

The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning for the project started after it was adopted in 1984 by the US government, and it officially launched in 1990. It was declared complete on April 14, 2003, and included about 92% of the genome. Level "complete genome" was achieved in May 2021, with a remaining only 0.3% bases covered by potential issues. The final gapless assembly was finished in January 2022.

<span class="mw-page-title-main">Edward Rubin</span> American geneticist

Edward Rubin is the chief scientific officer at Metabiota, a company that works on epidemic risk and infectious diseases. From 2002 to 2016, he was a researcher at the Lawrence Berkeley National Laboratory and the director of the Department of Energy's Joint Genome Institute. In 2012, he was named the Charles J. and Lois B. Epstein Visiting Professor at the University of California San Francisco.

<span class="mw-page-title-main">Integrated Microbial Genomes System</span> Genome browsing and annotation platform

The Integrated Microbial Genomes system is a genome browsing and annotation platform developed by the U.S. Department of Energy (DOE)-Joint Genome Institute. IMG contains all the draft and complete microbial genomes sequenced by the DOE-JGI integrated with other publicly available genomes. IMG provides users a set of tools for comparative analysis of microbial genomes along three dimensions: genes, genomes and functions. Users can select and transfer them in the comparative analysis carts based upon a variety of criteria. IMG also includes a genome annotation pipeline that integrates information from several tools, including KEGG, Pfam, InterPro, and the Gene Ontology, among others. Users can also type or upload their own gene annotations and the IMG system will allow them to generate Genbank or EMBL format files containing these annotations.

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References

  1. ↑ "DOE Joint Genome Institute". Berkeley Lab. Retrieved February 20, 2023.
  2. ↑ "BER User Facilities". US Department of Energy Office of Science. 9 December 2014. Retrieved February 20, 2023.
  3. ↑ "User Facilities". US Department of Energy Office of Science. 29 September 2020. Retrieved February 14, 2023.
  4. ↑ "User Facilities at a Glance". US Department of Energy Office of Science. 3 May 2022. Retrieved February 14, 2023.
  5. ↑ "Joint Genome Institute". U.S. Department of Energy Office of Science. 29 April 2022. Retrieved February 20, 2023.
  6. ↑ "DOE metrics/statistics". Joint Genome Institute. Retrieved February 20, 2023.
  7. ↑ "Our Science". Joint Genome Institute. Retrieved February 20, 2023.
  8. ↑ "User Programs". Joint Genome Institute. Retrieved February 20, 2023.
  9. ↑ "DOE Bioenergy Research Centers". Joint Genome Institute. Retrieved February 20, 2023.
  10. ↑ "Bioenergy Research Centers". U.S. Department of Energy. Retrieved February 20, 2023.
  11. ↑ "Strategic Management". Joint Genome Institute. Retrieved February 20, 2023.
  12. ↑ "Board Committee Members". Society for Industrial Microbiology and Biotechnology.
  13. ↑ "History". Joint Genome Institute. Retrieved 30 August 2022.
  14. ↑ "CSP Overview". Joint Genome Institute.
  15. ↑ "The Poplar Genome at 10". Joint Genome Institute. 15 September 2016.
  16. ↑ "Studying Sorghums Survival Skills". Joint Genome Institute. 24 June 2022. Retrieved February 20, 2023.
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