Walnut Creek, California
June 15, 2007
Toward the goal of harnessing the
power of nature through DNA sequencing, the DOE
Joint Genome Institute (DOE
JGI) has announced the latest Community Sequencing Program (CSP)
portfolio. These plant and microbial targets--most with
implications for helping wean the nation's dependence on fossil
fuel--total some 21 billion nucleotides of DNA sequence capacity
allocated to public projects submitted through the CSP for
fiscal year 2008.
"This year's selections are completely aligned with the CSP
mission, that is, selecting DOE-relevant organisms with the
large and diverse communities of investigators," said Jim
Bristow, DOE JGI Deputy Director and manager of the CSP. "The
response to this year's program, with over 120 submissions,
demonstrations an increasing desire to fuel discovery with DNA
sequence information--which DOE JGI makes freely available
through its web portals and the public databases."
Among the highest profile of these projects, and largest, with a
600-million-nucleotide genome, is the eucalyptus tree
genome--geared to the generation of resources for renewable
energy--led by Alexander Myburg of the
University of Pretoria, South
Africa, with Gerald Tuskan of Oak
Ridge National Laboratory (and DOE JGI), and Dario
Grattapaglia, of
EMBRAPA Genetic Resources and Biotechnology (Brazil).
"The biomass production and carbon sequestration capacities of
eucalyptus trees match DOE's and the nation's interests in
alternative energy production and global carbon cycling," said
Bristow. "The consortium of eucalyptus draws upon the expertise
from dozens of institutions and hundreds of researchers
worldwide."
"A major challenge for the achievement of a sustainable energy
future is our understanding of the molecular basis of superior
growth and adaptation in woody plants suitable for biomass
production," said CSP project proposer Myburg. Eucalyptus
species are among the fastest growing woody plants in the world
and, at approximately 18 million hectares in 90 countries, the
most widely planted genus of plantation forest trees in the
world. Eucalyptus is also listed as one of the U.S. Department
of Energy's candidate biomass energy crops.
"Genome sequencing is essential for understanding the basis of
eucalyptus's superior properties and to compare and contrast
them with other species," said Myburg. "The unique evolutionary
history, keystone ecological status, and adaptation to marginal
sites make eucalyptus an excellent focus for expanding our
knowledge of the evolution and adaptive biology of perennial
plants." The eucalyptus genome, the second tree to be sequenced,
will also provide extraordinary opportunities for comparative
genomic analysis with the poplar, the first tree sequenced,
published in the journal Science by DOE JGI and collaborators in
2006.
The second largest CSP project selected for 2008 is foxtail
millet (Setaria italica), led by researchers at the
University of Georgia, the University of Florida, the University
of Missouri, the U.S. Department of Agriculture Agricultural
Research Service - Cold Spring Harbor Laboratory, and the
University of Tennessee.
Foxtail millet, a forage crop, is a close relative of several
prospective biofuel crops, including switchgrass, napiergrass,
and pearl millet. In the U.S., pearl millet is grown on some 1.5
million acres. It is envisioned that pearl millet would be
useful as a supplement or replacement for corn in ethanol plants
in regions that suffer from drought and low-fertility soils.
The third largest genome project to be taken on by DOE JGI in
2008 is the marine red alga Porphyra purpurea. The ocean
plays a key role in removing carbon dioxide from the atmosphere
with the help of marine photosynthetic organisms like Porphyra
consuming the carbon and releasing oxygen. Porphyra species are
among the most common algae in the intertidal and subtidal zones
of temperate rocky shores in both the northern and southern
hemispheres. Understanding the effects of elevated climatic
stresses on photosynthetic organisms would benefit from
genome-enabled studies of carbon fixation in Porphyra, because
of this organism's great diversity of light-harvesting and
photo-protective strategies.
The CSP will pursue eight smaller eukaryotic projects in 2008,
using both traditional Sanger sequencing and next-generation
pyrosequencing technology. These projects include the following:
Paxillus involutus: Over 75
percent of the carbon in terrestrial ecosystems is stored in
forests. More than half of this carbon is found in soil
organic matter (SOM). Recent studies have indicated that
ectomycorrhizal fungi like Paxillus provide the dominant
pathway through which carbon enters the SOM. These fungi are
also known to protect plants from toxic metals. Thus, the
development of metal-tolerant fungal associations would
provide a strategy for active remediation of
metal-contaminated soils.
Two species of Phaeocystis
phytoplankton: The Phaeocystis genus contributes
approximately 10 percent of annual global marine primary
photosynthetic production, equivalent to four billion metric
tons of carbon dioxide captured or "fixed"
annually--reinforcing its importance for the study of the
global carbon cycle and carbon sequestration.
The leaf-degrading fungus
Agaricus bisporus: Genomic studies of A. bisporus target
enhanced understanding of the mechanisms employed for
efficient conversion of lignocellulose--crucial for the
production of fuels and products from renewable biomass.
The first ciliated
protozoan genome, Tetrahymena thermophila: A microbial model
organism for discovering fundamental principles of
eukaryotic biology, it will allow improved construction and
stability of cell lines for the over-expression of proteins,
including cellulase enzymes to overcome the limiting hurdle
of biomass-to-biofuel production and metal-chelating
proteins to enhance the already superior capacity of
ciliates for bioremediation of toxic heavy metals in
industrial effluents.
Pine and Conifer EST
resource: expressed sequence tags (ESTs) are fragments of
DNA sequence that serve as a tool for the identification of
genes and prediction of their protein products and their
function. Conifer forests are among the most productive in
terms of annual lignocellulosic biomass generation, and
coniferous trees are the preferred feedstock for much of the
forest products industry. Climate change and exotic forest
pests are threatening conifer populations. Breeding programs
to improve conifers will benefit from access to this genomic
resource.
The soybean pathogen
Heterodera glycines: Soybean is a major oil, feed, and
export crop, with $17 billion annually in unprocessed crop
value in the U.S. alone. Soy biodiesel is a leading
contender for a renewable, alternative vehicle fuel with a
high energy density. Soybean has the environmental and
energy advantage of not requiring the use of nitrogen
fertilizer. H. glycines is the most significant pathogen of
soybean in the U.S.; thus, sequencing its genome would aid
in the development of control strategies and directly
contribute to soybean yield enhancement.
The liverwort, Marchantia
polymorpha: The origin of land plants is acknowledged as one
of the major evolutionary events in the earth's history.
Experimental, paleontological, morphological, and molecular
systematic data all point to the liverworts as being among
the first plants to evolve and colonize the landscape. Thus,
liverworts are a key group to include in any comparative
study aimed at understanding the origin and evolution of
organisms that now cover much of terrestrial earth.
DOE JGI and its collaborators have
pioneered the emerging discipline of metagenomics--isolating,
sequencing, and characterizing DNA extracted directly from
environmental samples--to obtain a genomic and metabolic profile
of the microbial community residing in a particular environment.
In addition to adding 54 different microbial isolate genomes to
the production sequencing queue in 2008, DOE JGI will work with
large communities of collaborators to take on four important
metagenomic projects.
Anammox bacteria: Anammox
bacteria are able to synthesize the rocket fuel hydrazine
from ammonia and hydroxylamine. Insight into the genes and
proteins involved in this reaction may be the basis for
further optimization of the production of this potent fuel
in a suitable biological system. Also, anammox bacteria are
responsible for about 50 percent of the processing of
ammonia to nitrogen gas in the ocean. In marine ecosystems,
the carbon and nitrogen cycles are closely connected. More
information about the regulation and mechanism of CO2
sequestration by anammox bacteria in the ocean will
contribute to our understanding of the global biogeochemical
cycles and their impact on climate change.
Biogas-degrading community:
It is estimated that 236 million tons of municipal solid
waste is produced annually in the U.S., 50 percent of which
is biomass. Converting organic waste to renewable biofuel
represents an appealing option to exploit this potential
resource. In California alone, it is estimated that 22
million tons of organic waste is generated annually, which
if converted by microbial digestion, could produce biogas
equivalent to 1.3 million gallons of gasoline per day. Yet
little is known about the microorganisms involved and their
biology. This study aims to optimize the anaerobic digestion
process and promote conversion of biomass into biofuel.
Accumulibacter population
genomics: Enhanced biological phosphorus removal (EBPR) is a
wastewater treatment process used throughout the world to
protect surface waters from accelerated stagnation and
depletion of oxygen. EBPR can be unreliable and often
requires expensive backup chemical treatments to protect
sensitive receiving waters. This project will shed light on
the microbial population dynamics leading to better use and
management of these important environmental systems.
Genomics of Yellowstone
geothermal environments: The hot pools of Yellowstone
National Park harbor a mostly unexplored treasure-trove of
extremeophiles, microbes that thrive in extreme conditions.
These communities represent a rich opportunity to identify
enzymes or processes that promise to advance biofuels and
nanomaterial science applications.
Established in 2005, the Community
Sequencing Program (CSP) provides the scientific community at
large with access to high-throughput sequencing by 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 bioenergy, global carbon
cycling, and bioremediation.
For a full list of the CSP 2008 sequencing projects, see
http://www.jgi.doe.gov/sequencing/cspseqplans2008.html
The DOE Joint Genome Institute, supported by the DOE Office
of Science, unites the expertise of five national laboratories,
Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge,
and Pacific Northwest, along with the Stanford Human Genome
Center to advance genomics in support of the DOE mission related
to clean energy generation and environmental characterization
and clean-up. DOE JGI's Walnut Creek, Calif. Production Genomics
Facility provides integrated high-throughput sequencing and
computational analysis that enable systems-based scientific
approaches to these challenges. |
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