Feature Story | 10-Jun-2024

The Joint Genome Institute (JGI) advances genomic science as a pure data resource

As part of the Year of Open Science, the Department of Energy (DOE) Office of Science is highlighting our Public Reusable Research (PuRe) Data Resources

DOE/US Department of Energy

As part of the Year of Open Science, the Department of Energy (DOE) Office of Science is highlighting our Public Reusable Research (PuRe) Data Resources. The PuRe Data Resources are authoritative sources that make data easier to find, access, and reuse across the broader scientific community. In this article, we highlight the Joint Genome Institute (JGI).


Humans can learn a lot from nature, especially when dealing with climate change and other environmental issues. A clean energy future relies on us reducing our dependency on fossil fuels, breaking down waste, and storing atmospheric carbon. Biofuels made from decomposing living things or biological waste are a potential alternative to fossil fuels. Soil microorganisms can break down plant biomass to produce biofuels and bioproducts. Improving our understanding of these microorganisms is important for developing a U.S. bioeconomy.    

Scientists have studied the genetic systems of plants and soil microbes for decades. Using genetic engineering, scientists are able to selectively modify several types of microbes to produce biofuels and bio-based products. These microbes include whole cells of algae, fungi, and bacteria. These techniques require large amounts of high-quality, publicly available genomic information.

That’s where the Joint Genome Institute (JGI) shines. JGI is a Department of Energy (DOE) Office of Science user facility located at the DOE’s Lawrence Berkeley National Laboratory. It specializes in genomics science. This branch of science studies the structure, function, evolution, mapping, and editing of genomes, which is fundamental to understanding living systems. A genome is an organism’s complete set of DNA, including genes. 

JGI is a global leader in generating genome sequences of plants, microbes, and microbiomes. It supports about 15,000 users annually. The facility focuses on plant, fungi, and microbial species that are relevant to fulfilling DOE’s bioenergy and environmental missions. 

To unlock the secrets of genomics, JGI provides high-throughput DNA sequencing, DNA synthesis, and analysis services. While these services exist elsewhere, JGI brings together state of the art technologies, data, and a unique number and variety of tools as well as expertise. JGI also hosts a number of data portals. These portals make high quality data sets publicly available, allowing scientists to analyze, explore, and download this information. They provide a curated catalogue of genomic data and metadata. They also simplify research by assigning persistent identifiers to data objects for tracking data use and re-use. 

JGI has been a critical resource in several key applications: 

  • Biofuels: 30 percent of JGI’s sequencing capacity is dedicated to DOE’s Bioenergy Research Centers. Using multiple fungal genomes generated at JGI, scientists at the University of Illinois and BP (the oil and energy company) created and patented a process to improve how plants transport sugars. This technology can form the basis for large-scale ethanol production.
  • Impossible Meat: Mycotechnology, Inc. (the makers of Impossible Meat) has filed two patents for the production of sustainable meat substitutes that drew on data from JGI. The company leveraged JGI MycoCosm portal’s shiitake genome data and Phytozome’s protein data.
  • Targeting tumors: Using publicly available genomic information, researchers determined that a marine microbe can be an effective medication delivery tool for tumors in hard-to-reach areas of the brain. This discovery has roots in genomic data that JGI generated over 20 years ago. JGI data mapped out the genome of a microbe whose movements are influenced by geomagnetic fields.
  • Terraforming Mars: Researchers leveraged findings from JGI’s user science to determine that future space missions could use Cyanobacteria to produce oxygen for humans on Mars.

JGI aims to accelerate future scientific advances by creating a more integrated and collaborative data ecosystem. The team is working to bring together data from many different species, ecosystems, and experimental conditions. It is also aiming to create intuitive connections to related public data resources. These efforts will help the scientific community tackle climate and energy-related challenges. It will also enable new and innovative applications of JGI’s data.

The Office of Science is the single 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 the Office of Science website.

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