DOE Joint Genome Institute (JGI)
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is a DOE Office of Biological and Environmental Research (BER) genome science user facility. With the aim of leading
genomic
innovation for a sustainable
bioeconomy,
the JGI decodes the genetic information of plants, fungi,
microbes,
algae, and other targets relevant to DOE missions. The JGI provides access to high-throughput genomic capabilities and data analysis, helping researchers find solutions to energy and environmental research challenges to adapt and thrive under changing climate conditions. For example, many of the microbes in, on, and around the planet play roles in the
carbon cycle,
and other
nutrient cycles
are key to regulating the planet.
Working with the JGI
By decoding field samples collected from around the world, JGI users can learn from nature and apply the information to their research. (Image by Thor Swift/Berkeley Lab)
User Programs
The JGI serves a worldwide community of more than 2,000 primary users – those who apply for and gain access to JGI resources at no cost. The Community Science Program (CSP) supports the majority of JGI proposals, peer-reviewed for relevance to DOE missions. By learning about the genetic codes of organisms, many of these proposals aim to apply the data toward thriving in a warming world. For example, identifying plant traits that breeders could engineer to improve crop yields in conditions such as drought and
marginal soils,
and figuring out the genes of soil microbes that could help confer disease and pest resistance.
In working with the JGI, users gain access to not just scientific and technical capabilities and equipment, but the staff’s expertise as well. (Image by Thor Swift/Berkeley Lab)
Science Programs
Submitting a proposal to partner with the JGI doesn’t just mean access to the facility; collaborating researchers also avail of the staff’s scientific and technical expertise. They can work together to develop tools or processes within a project that can then be used not just by other users, but by the larger global research community. Many of the microorganisms remain unknown or cannot be studied because they have not been cultured in labs. To learn more, the JGI has developed techniques to decipher the genetic code of an organism from a single cell, or to learn more about microbes based on how they interact with their neighbors. These approaches have helped the global community learn more about these tiny but mighty players in environmental systems.
Mining JGI data portals for microbial and metagenome datasets allows researchers to learn more about the planet’s known microbial diversity – and find viruses that impact microbial health and the planet’s nutrient cycles. (Art by Zosia Rostomian/Berkeley Lab)
Data Science and Informatics
The data generated by the JGI are publicly accessible through several portals. Researchers can easily access and download public data sets for plants, fungi, algae, microbes, metagenomes, and
secondary metabolites
or work within these systems to conduct analyses. In 2022, alone, more than 15,000 data users worldwide downloaded over 4 million files from these JGI systems. JGI datasets may also be accessed and analyzed through partner portals such as the DOE Systems Biology Knowledgebase (KBase) and the National Microbiome Data Collaborative (NMDC). Both programs are BER-funded and co-located with the JGI at Lawrence Berkeley National Laboratory (Berkeley Lab).
TOUR THE JGI
The JGI is one of the 28 DOE Office of Science user facilities, located at Lawrence Berkeley National Laboratory in Berkeley, California. DOE’s BER program supports EMSL and several other user facilities, enabling users to conduct research related to the fundamental understanding and prediction of complex biological, Earth, and environmental systems for energy and infrastructure security.