The mission of the JGI is to provide genome sequencing, genome data acquisition, and genome analysis in support of the DOE mission needs in bioenergy, carbon cycling and biosequestration, and environmental remediation and stabilization.
The DOE-JGI was created in 1997 to carry out accurate, high throughput sequencing of human DNA in support of DOE's role in the Human Genome Project (HGP). With the completion of the HGP, the JGI sequencing capacity was refocused on the sequencing and analysis of genomes of the microbes, microbial communities (metagenomes) and other organisms (fungi, plants) important to the DOE mission. Since 2000, the JGI has served as a Scientific User Facility, inviting and responding to requests from the external scientific community for sequencing of microbial, plant, and other (non-human pathogen) targets. In all cases, the aim of the JGI is to provide to the national and international scientific community both the genome-derived "parts lists" as well as high quality computational analyses that support further discovery.
The DOE-JGI publishes an annual Community Sequencing Program solicitation for sequencing targets (see: http://www.jgi.doe.gov/CSP/overview.html). This program is typically open to letters of intent until mid-March each year. NOTE: The JGI does NOT provide funding support for sequencing or other research efforts. The Community Sequencing Program (CSP) provides the scientific community at large with access to high-throughput sequencing of significant scale at the DOE-JGI for projects of relevance to DOE missions. Sequencing projects are chosen based on scientific merit--judged through independent peer review--and relevance to issues in global carbon cycling, energy production, biogeochemistry and low dose radiation responses. Criteria for participation in this program, the review process, and interactions between JGI and participants are outlined at: http://www.jgi.doe.gov/CSP/user_guide/index.html). Through this program, the Department of Energy advances sequence-based scientific research from a broad range of disciplines. Three items to note:
1. CSP proposals for bacterial and archaeal isolates, to be submitted as brief white papers, will be accepted on a continuous basis, and will be reviewed every three months (typically early in February, May, August, and November of each year).
2. CSP proposals that utilize JGI's expanding capacity for new capabilities and new technology sequencing are encouraged. This includes large-scale metagenome sequencing, transcript profiling, DNA synthesis and resequencing of organisms for which reference genomes currently exist.
3. Proposals requesting sequencing of eukaryotic genomes will be considered but must include demonstration of genome size and polymorphism rate and should be supported by a significant user community.
The three primary thrusts of this year's CSP are:
a) Plant and Plant-Microbe Interactions: Studies are encouraged that explore the interaction of plants with their rhizosphere communities and other microbes or fungi that affect bioenergy-relevant plant phenotypes. Plant resequencing or transcriptomic projects are of interest but whole-genome de novo plant sequencing projects are discouraged for this CSP call.
b) Microbial emission and capture of greenhouse gases: Studies are sought that will provide insight into global carbon, nitrogen, and methane cycles, and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction from environmental sources based sequencing of fungi, bacteria, or algae.
c) Metagenomics: Proposals are encouraged that couple metagenomic analyses with measures of the active component of microbial populations and associated environmental biogeochemistry to explore dynamic changes in the active community composition and expressed metabolism of microbial communities in DOE mission-relevant areas.
Why the Program's Research is Important
The genome sequence of any organism, from a virus to an entire multi-species community, provides a catalogue of the component "working parts". The knowledge of that "parts list" is a fundamental starting point for a powerful array of biological investigations to describe and predict cellular functions and cellular or community responses to changing environments as well as to explore biological approaches to achieving mission-critical goals. Comparative genome and community genome (metagenome) studies also contribute towards understanding fundamental principles of the control circuits regulating gene expression and action and learning how external signals (environmental, hormonal, chemical, etc.) govern cellular and community processes. Transcriptome sequencing can reveal how a cell or community uses its genomic information by showing patterns of gene expression in response to stimuli.
Data Sharing Policy
The DOE-JGI data release policy is accessible at: http://my.jgi.doe.gov/general/datarelease.html
Sequencing of submitted projects by the program is contingent on adherence to this data sharing policy. It is also expected that organisms sequenced by the JGI will be deposited in public repositories to ensure public access to sequenced strains.
More Information about the Program and Its Accomplishments
DOE-JGI Site: http://www.jgi.doe.gov/
Dan Drell, Ph.D.
Biological Systems Science Division, SC-23.2
U.S. Department of Energy, GTN Bldg.
1000 Independence Avenue, SW
Washington, DC 20585-1290
Phone: (301) 903-4742
Fax: (301) 903-0567