The U.S. Department of Energy

United States Department of Energy

The United States Department of Energy is a Cabinet-level department of the United States government concerned with the United States' policies regarding energy and safety in handling nuclear material...

 (DOE) Joint Genome Institute (JGI) was created in 1997 to unite the expertise and resources in genome

Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

 mapping, DNA sequencing

DNA sequencing

DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....

, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory

Lawrence Berkeley National Laboratory

The Lawrence Berkeley National Laboratory , is a U.S. Department of Energy national laboratory conducting unclassified scientific research. It is located on the grounds of the University of California, Berkeley, in the Berkeley Hills above the central campus...

 (LBNL), Lawrence Livermore National Laboratory

Lawrence Livermore National Laboratory

The Lawrence Livermore National Laboratory , just outside Livermore, California, is a Federally Funded Research and Development Center founded by the University of California in 1952...

 (LLNL) and Los Alamos National Laboratory

Los Alamos National Laboratory

Los Alamos National Laboratory is a United States Department of Energy national laboratory, managed and operated by Los Alamos National Security , located in Los Alamos, New Mexico...

 (LANL). The DOE JGI also collaborates with other national labs such as Oak Ridge National Laboratory

Oak Ridge National Laboratory

Oak Ridge National Laboratory is a multiprogram science and technology national laboratory managed for the United States Department of Energy by UT-Battelle. ORNL is the DOE's largest science and energy laboratory. ORNL is located in Oak Ridge, Tennessee, near Knoxville...

 (ORNL) and Pacific Northwest National Laboratory

Pacific Northwest National Laboratory

Pacific Northwest National Laboratory is one of the United States Department of Energy National Laboratories, managed by the Department of Energy's Office of Science. The main campus of the laboratory is in Richland, Washington....

 (PNNL).

In 1999, the University of California

University of California

The University of California is a public university system in the U.S. state of California. Under the California Master Plan for Higher Education, the University of California is a part of the state's three-tier public higher education system, which also includes the California State University...

, which manages the three national labs for the DOE, leased laboratory and office space in a light industrial park in Walnut Creek, California

Walnut Creek, California

Walnut Creek is an incorporated city located east of the city of Oakland. It lies in the East Bay region of the San Francisco Bay Area. While not as large as neighboring Concord, Walnut Creek serves as the business and entertainment hub for the neighboring cities within central Contra Costa...

 to consolidate genome research activities. Led by Eddy Rubin

Edward Rubin

Edward M. "Eddy" Rubin is an internationally known geneticist and medical researcher at the Lawrence Berkeley National Laboratory in Berkeley, California and has served as the director of the Department of Energy's Joint Genome Institute since 2002...

, M.D., Ph.D., the DOE JGI receives its funding from the Office of Biological and Environmental Research in DOE's Office of Science.

Originally established to work on the Human Genome Project

Human Genome Project

The Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...

--the DOE JGI generated the complete sequences of Chromosomes 5, 16 and 19—the DOE JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the DOE's science mission. Since 2004, the DOE JGI has been a user facility that advances genomics research in a broad range of disciplines where DNA sequence information is likely to drive scientific discoveries.

In February 2004, the DOE JGI launched the Community Sequencing Program (CSP), which provides the scientific community at large with access to high-throughput, high-quality sequencing. Sequencing projects involve many important multicellular organisms, microbes and communities of microbes called metagenomes related to the DOE mission areas of bioenergy, understanding global cycles such as the carbon cycle

Carbon cycle

The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth...

 and biogeochemistry

Biogeochemistry

Biogeochemistry is the scientific discipline that involves the study of the chemical, physical, geological, and biological processes and reactions that govern the composition of the natural environment...

, and are chosen based on outside scientific review.

Microorganisms such as those that thrive under extreme conditions such as high acidity, radiation and metal contamination are of particular interest to the DOE. Investigations by the DOE JGI and its partners are shedding light on the cellular machinery of microbes and how they can be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere and produce potentially important sources of energy such as hydrogen and methane.

In 2006, the DOE JGI published the genome of the first tree sequenced--the cottonwood (Populus trichocarpa

Poplar

Populus is a genus of 25–35 species of deciduous flowering plants in the family Salicaceae, native to most of the Northern Hemisphere. English names variously applied to different species include poplar , aspen, and cottonwood....

). In partnership with other federal institutions and universities, the DOE JGI has also published the genome sequences of sorghum; the microbial community in the termite hindgut, which could provide enzymes useful to biofuel production; microbes such as the bacteria Desulfovibrio that clean up sites contaminated with radioactive or toxic compounds; and algae involved in the global carbon cycle that are being used to track the effects of climate change in the oceans.

In 2009, the DOE JGI announced several dozen sequencing projects approved for CSP 2010. They include the microbial community inside the desert locust gut, bacteria that taint wine, fungi that can break down lignin

Lignin

Lignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae. The term was introduced in 1819 by de Candolle and is derived from the Latin word lignum, meaning wood...

 and cellulose

Cellulose

Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....

, radiation-resistant bacteria, and microbial communities in the Alaskan permafrost, Nevadan hot springs and within earthworm egg capsules.

With sequencing capacity of more than a trillion bases generated annually, a full fifth of the genome projects at sequencing centers worldwide are done by the DOE JGI. The DOE JGI makes the high-quality genome sequencing data generated freely available to the greater scientific community through its web portal and on public databases.

The DOE JGI also supports programs dedicated to functional and evolutionary genomics related to the organisms and environments being sequenced and the development of computational and bioinformatic tools for data management and mining. One such program is the Integrated Microbial Genomes System

Integrated Microbial Genomes System

The Integrated Microbial Genomes is a genome browsing and annotation system developed by the DOE-Joint Genome Institute. IMG contains all the draft and complete microbial genomes sequenced by the DOE-JGI integrated with other publicly available genomes...

(IMG), which provides a framework for comparative analysis of primarily microbial genomes, though the system also supports eukaryotic genomes and environmental samples. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective.

External links and sources

• Joint Genome Institute (official)
• Lawrence Livermore National Laboratory (official)
• Lawrence Berkeley National Laboratory (official)
• Los Alamos National Laboratory (official)