Mission

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory (Berkeley Lab) and part of the Biosciences Area.

Supported by the DOE Office of Science, the JGI unites the expertise at Berkeley Lab, Lawrence Livermore National Laboratory and the HudsonAlpha Institute for Biotechnology. We are located in the Integrative Genomics Building in the heart of the Berkeley Lab campus, atop the hills above Berkeley, California and operated by the University of California for the U.S. Department of Energy. 

The JGI provides integrated high-throughput sequencing, DNA design and synthesis, metabolomics and computational analysis that enable systems-based scientific approaches to these challenges.

Our homepage video includes external footage from: 

• University of Delaware
• Laura.Selbmann©PNRA. All the sampling activities in Antarctica have been performed in the frame of italian expeditions of the Italian National Program for Antarctic Researches (PNRA),  funded by the Italian Ministry of University and Research; all specimens collected and fungi isolated are preserved in the Culture Collection of Fungi from Extreme Environment, the Italian National Antarctic Museum (MNA-CCFEE).

The JGI was created in 1997 to unite the expertise and resources in DNA sequencing, informatics, and technology development pioneered at the U.S. DOE genome centers at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory. 

In 1999, to accelerate the completion of DOE’s commitment to the Human Genome Project, the University of California, which manages Berkeley Lab, leased laboratory and office space in a light industrial park in Walnut Creek, California, to consolidate activities. The significant economies of scale achieved in doing so enabled the JGI to be the first to publish the sequence analysis of the target chromosomes 5, 16, and 19, in the journal Nature. Following this accomplishment, the JGI went on to advance basic science by sequencing scores of microbial species as well as several model organisms and contributing this information freely to the public databases.

In 2004, the JGI established itself as a national user facility, and has grown to serve a worldwide community of more than 2,000 primary users—those who apply for JGI resources and are engaged in active projects—each year. In addition, several thousand data users worldwide download millions of files. 

The vast majority of JGI proposals are supported under the auspices of our Community Science Program, characterize organisms (plants and microbes) relevant to the DOE science mission areas of bioenergy and environmental microbiome processes. 

Among the JGI’s largest dedicated partnerships are the DOE Bioenergy Research Centers, which seek to accelerate the development of biofuels and bioproducts. The JGI continues to receive its support from the Biological and Environmental Research program in the DOE’s Office of Science.

In December 2019, the JGI relocated to the newly-built Integrative Genomics Building (IGB), a home it shares with the staff of the DOE Systems Biology Knowledgebase (KBase) and the National Microbiome Data Collaborative (NMDC) in the heart of the Berkeley Lab.

The DOE’s Biological and Environmental Research (BER) program manages the JGI. The JGI provides genomic capabilities to the user community in support of BER’s bioenergy and environmental missions. 

These missions align with the DOE’s Biological and Environmental Research (BER) program priorities for seeking to understand functional principles that drive living systems, from microbes and microbial communities to plants and other whole organisms with systems biology approaches for:

• developing renewable and sustainable sources of biofuels and bioproducts from plant biomass,
• understanding the biological processes controlling greenhouse gas accumulation in the atmosphere (especially carbon dioxide and methane),
• gaining insights into biogeochemical processes that control the cycling of key nutrients in environments for sustainable bioenergy production or the mobility of heavy metals and radionuclides at contaminated sites for which DOE has stewardship responsibilities,
• and leveraging microbiomes for beneficial purposes. 

Projects focused on organisms for comparative purposes, on model systems for microbe-microbe or plant-microbe interactions, or on development of improved sequencing-based technologies are also welcomed but the applicant should clearly outline how the proposed work will advance BER-mission relevant science. 

Projects primarily focused on human health, food/animal agriculture, wastewater treatment, or bioremediation of organics will not be considered. Projects targeting marine systems must clearly demonstrate relevance and translatability to freshwater, coastal or terrestrial systems.
Additional information about DOE’s Biological and Environmental Research program mission can be found at http://science.energy.gov/ber/.

The United States is one of the world’s largest consumers of petroleum, most of which is used for transportation and industry. Petroleum is also the starting material for the production of almost all plastics. This drives the DOE’s focus on developing lignocellulosic biomass as a clean, renewable and sustainable alternative source for biofuels and bioproducts.

Such biofuels would ideally offer energy content on par with gasoline, diesel, and aviation fuels, while being compatible with our existing fuel distribution infrastructure. Sequencing, DNA synthesis, and metabolomics projects at the JGI that contribute to meeting this goal focus on one of three categories:

• terrestrial plants that can be used as feedstocks for biofuel and bioproduct production and their associated microbiomes;
• fungi, microbes and microbial communities that can break down the lignin and cellulose in plant walls;
• and organisms that can convert lignocellulosic-derived sugars or lignols into biofuels or other bioproducts currently produced from petroleum (excluding pharmaceutical, cosmetic, and food products).

Microbes constitute the largest reservoir of biodiversity on Earth. Their activities and interactions are at the core of many environmental processes, and the genetic makeup of microbial species and communities forms the basis of their behavior in the environment. 

The JGI genome sequences and metabolomes of microbes and microbial communities significantly contribute to element and nutrient cycling, particularly those found in less well-understood terrestrial, subsurface, and terrestrial-aquatic interface ecosystems. JGI also focuses on projects that aim to understand biogenic contributions to the global carbon cycle, as well as atmospheric particle formation and evolution. 

Data from such studies is expected to contribute to better predictive models of global climate. They may also provide a basic understanding of the roles microbiomes play in determining the behavior of the physical environment and provide opportunities for biologically-based mitigation strategies.

The JGI seeks to support projects that will foster a genome-enabled understanding of microbial behavior with an impact on the physical, chemical, and geochemical processes that control the environmental fate of key elements with an impact on BER’s energy and environmental mission objectives.

Fungi, algae, bacteria, archaea, viruses, and microbial communities of interest to the JGI as sequencing, DNA synthesis, and metabolomics targets include:

• those involved in elemental and nutrient cycles,
• those that impact sustainable bioenergy crop growth or global carbon cycling, and
• and those involved in the cycling of elements that mediate the transformation of or are energetically coupled to contaminants such as heavy metals or radionuclides in soils, freshwater, coastal sediments (coastal here defined by NOAA as the area within 185 km/100 nautical miles of land), and the subsurface.