The genome—an organism’s complete set of genetic material written in the language of DNA code— contains the biological instructions required to build and maintain a living system. By providing the research community with access to the latest generation of genome sequencing and analysis capabilities, the Department of Energy (DOE) Joint Genome Institute (JGI) user facility is enabling scientists worldwide to investigate the biological blueprints of an ever-increasing array of microbes, fungi, plants, and environments important to DOE missions.
Producing genomic profiles of complex environmental samples and assembling high-quality reference sequences for plant genomes that can be many times larger than the human genome or any known animal genome are just some of the sequencing challenges unique to DOE. These challenges demand the blend of computational resources, expert staff, automated processing pipelines, and diverse sequencing technologies that only a facility like JGI can provide. Located in Walnut Creek, California, the DOE JGI’s partner institutions include five national laboratories and one nonprofit biotechnology institute. The JGI is supported by the Office of Biological and Environmental Research in DOE’s Office of Science.
From helping users plan and scope projects to providing tools for analyzing and annotating sequence data, the DOE JGI offers researchers comprehensive, end-to-end resources.
Leveraging Advanced Technologies for DNA Sequencing. A seismic technological change is presently under way in the field of genomics. New technologies used at the DOE JGI can sequence many more samples much faster. Each of these next-generation sequencing machines can produce in just a few days what the entire JGI facility once yielded in a month.
Giving Raw DNA Sequence Biological Meaning. Once the order of the millions or billions of DNA bases is determined for a genome project, JGI researchers computationally locate and identify genes and other regions of biological significance within the sequence. The advanced computational resources and the development of scalable software infrastructures at JGI’s national laboratory partners provide robust support for this process of annotating the exploding volume of genomic data.
Developing and Sharing Resources for Genome Analysis. The DOE JGI continues to expand and improve its genome browser and comparative data analysis portals for microbes (IMG, the Integrated Microbial Genomes system) and for plants (phytozome.net). These portals provide a unified “onestop shop” for genomic data, enabling users to navigate across genomes, gene repertoires, and pathways; to perform increasingly complex and customized queries and analyses over the web; and to integrate opensource software with JGI-developed comparative algorithms.
Setting Standards for Generating and Analyzing Genome Sequence. In addition to working with other sequencing centers to standardize definitions and protocols for producing high-quality sequence data, the DOE JGI plays a leading role in establishing data and metadata standards for plant genomes and for metagenomes1 (DNA isolated from microbial and microbial-plant communities). As DNA and RNA are isolated from a broadening range of exotic environments, an important need for representing “metadata” is the development of an appropriately rich set of standards that captures the relevant variables for each sample.
1 Chain, P. S. G., et al. 2009. “Genome Project Standards in a New Era of Sequencing,” Science 326(5950), 236–37.
Facilitating Interdisciplinary Discussion, Cooperation. Furthering its role as a world-class sequencing and analysis facility, the DOE JGI holds an annual users meeting where researcher insights enabled by genomic sequences are discussed among interdisciplinary scientists working on diverse biological challenges. Prior to the meeting, the JGI holds several workshops focusing on specific sequencing projects.
JGI’s Community Sequencing Program (CSP) is designed to bring high-throughput sequencing to the scientific community at large. Sequencing projects are chosen based on scientific merit, judged through independent peer review and relevance to issues in global carbon cycling, alternative energy production, and biogeochemistry. Proposals for bacterial and archaeal isolates may be submitted at any time as brief white papers and are reviewed every 3 months.
The DOE JGI unites the expertise of five national laboratories and one nonprofit biotechnology institute: