WALNUT CREEK, CA–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, demonstrates 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.
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.