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Checkbiotech: DOE JGI announces 2006 Community Sequencing Program portfolio
Posted by: DR. RAUPP ; madora (IP Logged)
Date: May 15, 2005 10:22AM ; ;

Embedded in the language of DNA, the common link among all living things,
are lessons for interpreting the complex systems that regulate the health of
planet Earth. Now, rounding out this global lesson plan are more than 40 new
genome projects, representing a cornucopia of life forms, from the important
grain sorghum, to catfish, crustaceans, and a host of extreme lifestyle
microbes, slated for DNA sequencing by the U.S. Department of Energy (DOE)
Joint Genome Institute (JGI, May 2005 by David Gilbert.

"Through the Community Sequencing Program, we are leveraging the dramatic
advances in genomic technology accrued since DOE launched the Human Genome
Project nearly 20 years ago," said Dr. Raymond L. Orbach, director of the
DOE Office of Science. "Our ability to generate DNA sequence, particularly
over the last three years, has approached Moore's Law proportions--in
effect, doubling every 18 months. These advances have enabled DOE JGI to
emerge as one of the preeminent contributors to microbial and plant

"The Community Sequencing Program will provide tremendous value," said Dr.
Aristides Patrinos, associate director of science for Biological and
Environmental Research, "because it will serve the high priority sequencing
needs of the broader scientific community while attracting scientists from
many disciplines to study and solve problems that are important to the DOE
missions of clean energy, bioremediation, and carbon sequestration."

The DOE JGI, already among the most productive genome sequencing centers in
the world with more than 225 organisms to its credit, is poised to add
significantly to this total and to the scientific literature through its
Community Sequencing Program (CSP).

With the 2006 CSP allocation, DOE JGI will be making freely available to the
greater scientific community 20 billion letters of genetic code (bases),
roughly the equivalent of nearly seven human genomes of information. This
year 135 proposals were submitted, nearly a 2.5-fold increase from the CSP's
inaugural call for proposals in 2004.

The largest single genome selected this year, the tropical grain Sorghum
bicolor, proposed by an international consortium led by researchers at the
University of Georgia and Rutgers, The State University of New Jersey, will
complement the knowledge already gleaned from rice, the only other monocot
grain to have been sequenced to date. Sorghum, with its economic importance
worldwide exceeding $69 billion per year, is expected to provide an improved
blueprint for the study of other important grains such as maize, millet, and
sugarcane. Sorghum, with a relatively compact genome of approximately 736
million bases, will serve as a valuable reference for analyzing the
four-fold larger genome of maize, the leading U.S. fuel ethanol crop.
Sorghum is an even closer relative of sugarcane, arguably the most important
biofuels crop worldwide, with annual production of about 140 million metric
tons with a value approaching $30 billion.

The Sorghum genus also includes one of the world's most noxious weeds. The
same features that make the weedy "Johnson grass" (S. halepense) so
tenacious are actually desirable in many forage, turf, and biomass crops.
Thus, sorghum offers novel learning opportunities relevant to weed biology
as well as to crop improvement.

Another CSP large genome target, Mimulus guttatus, the common or "seep
spring" monkey flower, although not a food crop, is a relative not too
distant from the likes of tomato, potato and other dicot, or broadleaf,
crops. Researchers from Duke University, who proposed the project, believe
it is reasonable to expect the molecular genetic basis of the monkey
flower's path of evolution and adaptation could be readily transferable to
crop plants.

"By sequencing the monkey flower, DOE JGI will be enabling genomicists to
pioneer new territory, taking on one of the most difficult and fundamental
questions in evolutionary biology--how new species evolve," said Dr. Richard
A. Jorgensen, associate professor of plant sciences at the University of
Arizona, and editor-in-chief of The Plant Cell. "The genus Mimulus is a
fantastic model system for this problem, exhibiting two different types of
speciation, one being the evolution of pollinator specificity and the other
being the evolution of mating systems."

M. guttatus is also quite tolerant of soil conditions that would be toxic to
other plants. For instance, the species thrives on soils composed of
California's state rock-- serpentine--which contains high levels of
magnesium, nickel, and manganese. Sequencing the monkey flower promises a
better understanding of how plants can help remediate soil contaminated with
toxic metals.

One of DOE's most enduring goals is to replace fossil fuels with renewable
sources of cleaner energy, such as hydrogen produced from plant biomass
fermentation. The lowly termite is actually one of the planet's most
efficient bioreactors, capable of cranking out two liters of hydrogen from
fermenting just one sheet of paper. Termites accomplish this Herculean task
by exploiting the metabolic capabilities of microorganisms inhabiting their
hindguts. DOE JGI will be sequencing this community of microbes to provide a
better understanding of the biochemical pathways used in the termite
hindgut, which may lead to more efficient strategies for converting biomass
to fuels and chemicals. Similarly, an ability to harness the pathways
directly involved in hydrogen production in the termite gut may one day make
biological production of this alternative energy source a viable option.

DOE JGI also will be casting deep into the aquatic gene pool--sequencing
genes from two species of catfish, the Channel catfish (Ictalurus punctatus)
and the blue catfish, (I. furcatus). Catfish is a two billion dollar
industry annually in the United States alone, representing 68 percent of all
aquaculture production.

In addition, the CSP will facilitate the sequencing of five species of fish
of the family Cichlidae from the Lake Malawi in east Africa. Popular food
fish and aquarium specimens, Cichlid fish have undergone an astonishingly
rapid proliferation of species from this evolutionarily fertile source. Over
the last two million years, some 700 species have emerged from the depths of
Lake Malawi.

Other CSP projects of note include:
- Arabidopsis lyrata and Capsella rubella, two mustard relatives whose
sequence will shed light on the genetics, physiology, development, and
structure of plants in general and how they respond to disease and
environmental stresses;
- A metagenomic community of waste-degrading bacteria capable of treating
industrial streams contaminated with terephthalate, a major byproduct of
plastics manufacturing;
- A community of Korarchaeota, a group of Archaea, the least well
characterized of the three domains of life, obtained from Obsidian Pool hot
spring in Yellowstone National Park;
- Six members of the Crenarchaeota group of Archaea, including
Methanocorpusculum labreanum, isolated from surface sediments of La Brea Tar
Pits in Los Angeles, which present features allowing proteins to function at
extremes of temperature, acid, and salinity;
- A powerful fungal pathogen--Mycosphaerella fijiensis--cause of black
Sigatoka--currently regarded as one of the most serious threats to world
banana production;
- Mytilus californianus, the edible pacific mussel that is a sentinel
species for environmental pollution;
- Triphysaria versicolor, a parasitic plant that releases chemicals into the
soil that affect the growth and development of nearby plants, a phenomenon
known as allelopathy, which could be used to control unwanted vegetation;
- The soil-dwelling fungal microorganism Trichoderma virens that also has
promise for biological weed control;
- Petrolisthes cinctipes, the porcelain crab, whose heat and cold tolerance
will help inform climate change research;
- Bicyclus anynana, a butterfly whose sequence encodes wing patterns that
should reveal key issues in evolutionary-developmental biology, and provide
information that will bolster efforts to understand biological diversity.


The full roster of CSP organisms can be found at:

The DOE Joint Genome Institute, supported primarily by the Department of
Energy Office of Biological and Environmental Research in the DOE Office of
Science, is among the world leaders in whole-genome sequencing projects
devoted to microbes and microbial communities, model system vertebrates,
aquatic organisms, and plants. Established in 1997, JGI now unites the
expertise of four national laboratories, Lawrence Berkeley, Lawrence
Livermore, Los Alamos, and Oak Ridge, along with the Stanford Human Genome
Center to advance the frontiers of genome sequencing and related biology.
Additional information about JGI can be found at []

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