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Joint Genome Institute Targeting Energy Crops for Sequencing

12 July 2006

Bioenergy crop plants switchgrass and cassava, other important agricultural commodities such as cotton, and microbes geared to break down plant material to render biofuels, round out the roster of more than 40 projects for genetic sequencing to be tackled by the US Department of Energy Joint Genome Institute (DOE JGI) over the next year.

The genomes of these organisms will be sequenced and characterized as part of the DOE JGI Community Sequencing Program (CSP). More than 15 billion letters of genetic code—the equivalent of the human genome five times over—will be processed through the DNA sequencers at the DOE JGI Production Genomics Facility for this year’s program.

By coupling DNA sequencing technology with fundamental research, we seek to make cellulosic ethanol a major part of the nation’s energy future.

—DOE JGI Director Eddy Rubin

Rubin’ remarks and the CSP selections echo recommendations outlined in the Breaking the Biological Barriers to Cellulosic Ethanol report earlier issued by DOE. (Earlier post.)

Switchgrass has enormous potential as an energy crop and environmental benefits that are associated with its cultivation. I envision that switchgrass will be an important feedstock for the emerging lignocellulose to ethanol industry. An enhanced understanding of gene structure and diversity at the molecular level may lead to new approaches to enhance both biomass productivity and feedstock quality for bioenergy production.

—Chris Somerville, Stanford University and the Carnegie Institution

In complement to switchgrass, DOE JGI will be sequencing Brachypodium distachyon, a temperate grass model system with a simple genome more amenable to sequencing. This choice responds to the urgent need for developing grasses into superior energy crops and improving grain crops and forage grasses for food production.

Brachypodium will be undertaken via a two-pronged strategy: the first, a whole-genome shotgun sequencing approach, a collaboration between John Vogel and David Garvin, both of the USDA, and Michael Bevan at the John Innes Centre in England; and the second, an expressed gene sequencing effort, led by Todd Mockler and Jeff Chang at Oregon State University, with Todd Michael of The Salk Institute for Biological Studies, and Samuel Hazen from The Scripps Research Institute.

Another major CSP project is the selection of cassava (Manihot esculenta), an excellent energy source and food for approximately one billion people around the planet. Its roots contain 20 to 40% starch from which ethanol can be derived, making it an attractive and strategic source of renewable energy. Cassava grows in diverse environments, from extremely dry to humid climates, acidic to alkaline soils, from sea level to high altitudes, and in nutrient-poor soil.

Sequencing the cassava genome will help bring this important crop to the forefront of modern science and generate new possibilities for agronomic and nutritional improvement. It is a most welcome development.

—Norman Borlaug, Nobel laureate, father of the “Green Revolution,” and Distinguished Professor of International Agriculture, Texas A&M University.

The cassava project will extend benefits to its vast research community, including a better understanding of starch and protein biosynthesis, root storage, and stress controls, and enable crop improvements, while shedding light on such mechanisms shared by other important related plants, including the rubber tree and castor bean.

The cassava project, led by Claude M. Fauquet, Director of the International Laboratory for Tropical Agricultural Biotechnology and colleagues at the Danforth Plant Science Center in St. Louis, and includes contributions from the USDA laboratory in Fargo, ND; Washington University St Louis; University of Chicago; The Institute for Genomic Research (TIGR); Missouri Botanical Garden; the Broad Institute; Ohio State University; the International Center for Tropical Agriculture (CIAT) in Cali, Colombia; and the Smithsonian Institution.

Adding to the list of crops to be sequenced by DOE JGI is the oyster mushroom, Pleurotus ostreatus, for its prospective role in bioenergy and bioremediation. This white-rot fungus is an active lignin degrader in the forests.

Lignin, a poly-aromatic hydrocarbon, is the second most abundant biopolymer on earth and its breakdown is a necessary step for making cellulose—the most abundant carbon biopolymer—available for conversion to biofuels.

This organism will serve as a valuable comparison to the reference genome of white-rot fungus Phanerochaete chrysosporium, previously sequenced by DOE JGI, which belongs to a different phylogenetic branch and carries a different set of ligninolytic enzymes. Understanding the whole-genome regulation of the P. ostreatus will add further value in that its lignocellulolytic enzymes could facilitate bioremediation and other biotechnological processes.

The poly-aromatic hydrocarbon oxidizing enzymes present in P. ostreatus can participate in the biodegradation of dyes, of contaminating wastes produced in agroindustries, and of forest, pulp and paper industrial by-products. This project is led by Antonio Pisabarro of the Public University of Navarre, Spain and includes more than a dozen other institutions including University of Wisconsin, Michigan State, Texas A&M, Duke, and Southeast Missouri State.

The CSP has tapped important projects from the most extreme locales, including the pristine cold environment described by a system of lakes in the Vestfold Hills region of Antarctica. This project, led by Rick Cavicchioli of the University of New South Wales in Sydney, Australia, seeks to define a microbial model for the biogeochemical process that take place in extreme cold conditions.

This project entails the strategy of metagenomics, pioneered by DOE JGI, for isolating, sequencing, and characterizing DNA extracted directly from environmental samples. These data are then used to define a profile of the microbial community residing in a particular environment.

Microbes constitute as much or more of the living mass on this planet than do the “higher forms”. Microbes are absolutely basal to the great flows of organic matter and energy that underlie the biosphere; without them macroscopic life on this planet is impossible. In other words, the existence of macroscopic life is totally conditioned upon the prior and continued existence of microbial life. You can see why the proposed work delights an old evolutionist like myself. Here you see the microbial world in its full glory—its true significance to the biosphere, and so to mankind. Here is the microbiology of the 21st century.

—Carl Woese, University of Illinois at Urbana-Champaign

The genomic and functional data gleaned from the Antarctic environmental samples, linked to meteorological, geological, chemical and physical data, will provide a better understanding about how these microorganisms have evolved, transformed, and presently interact with their frigid environment. These studies, while basic to understanding how microbes cope with environmental challenges, also seek to unlock the potential of cold-adapted microbes as sources of fuel, for example, transforming carbon dioxide effluent into methane.

Plant pests are the target of another international collaboration, linking researchers in Sweden, France, Norway, Germany, Canada and at the University of California, Berkeley. Heterobasidion annosum is the most economically devastating forest pathogen in the northern hemisphere, causing root rot in conifers, a major renewable biological energy resource.

These forests support biodiversity and serve as an important CO2 sink buffering global climate change. Improved knowledge of this tree pathogen will help build strategies to protect these wooden resources and enable a better understanding of important enzymatic systems involved in oxidation and degradation of polyphenolic substances—pollutants that are targets for bioremediation.

Actinobacteria, which can be found in soil, can be harnessed for environmental clean-up as well. Strains, the subject of another CSP project, proposed by researchers at the Swedish University of Agricultural Sciences and Hebrew University, have promise for the development of environmentally sound, cost effective biological strategies to reduce environmental pollution.

Resources:

  • Full list of the CSP 2007 sequencing projects

July 12, 2006 in Biotech, Cellulosic ethanol, Fuels | Permalink | Comments (7) | TrackBack (1)

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Comments

Its my opinion that if we are to grow our own fuel (of which I am not convinced that we can ever do), we need to use a naturally growing plant, and not introduce some genetically derived plant to replace what grows naturally. (There was an earlier post about using naturally growing mesquite in Texas, as a biofuel feed.)

There seems to me to be the problems of the genetically modified plant being duluted/cross linked with whatever grows naturally, making the process less efficient over time.

I disagree. By bio-engineering plants we can make ones which more efficently produce biofuels.

There is no doubt that with time and sufficient efforts and resources we can diversify/improve feedstocks, cellulose extraction and conversion to ethanol/n-butanol and other biofuels.

On the other hand, is there enough land to feed 7+ billion people and 7+ billion gas (ethanol/n-butanol) guzzlers?

Wouldn't it be wiser to feed people with our land. Streamline and electrify our vehicles and feed them with clean energy from the sun/wind/waves and even from improved nuclear power plants. Use PHEVs for now (or very near future) and EVs when ESDs (Electricity Storage Devices), i.e batteries and ultra-caps are sufficiently improved.

A manageable quantity of cellulosic ethanol/n-butanol/biofuels could be produced for special applications, mainly airborne vehicles and ships.

The use of fossil liquid fuels should be curtailed with the application of a progressive discouraging carbon tax + import duties.

While genetic modified organisms (GMO) hold great promise, we have to be very careful. An early attempt to use GMO's to breakdown cellulose into ethanol created a bacteria that caused plants to die when the left over mash was applied to the soil. What if we are too successful at creating a prolific species of switchgrass that spreads like dandilions? How do we put the genie back in the bottle if the manmade plant causes bigger problems than the original problem it was intended to solve? Our record at getting rid of invasive species once they are introduced is not very good (Duckweed, starlings, zebra mussels, etc.)

I couldnt agree more with James White. New species of plants introduced into areas where they are not native, has caused many problems in the past. Sometimes, just as simple as crowding out the native plants allowing them to die out. In otherwords, turning into a weed which is hard to control.

I also somewhat agree with Harvey D. That should be the ultimate goal. But how do we get to that point without turning the whole economy upside down? We must adapt and modify to get, to the ultimate goal. We must slow down, drive less, and eliminate waste and excess at every oportunity. Reimpose the 55mph speed limit, and enforce it? Not with this congress, or any other of the past 25 years.

Back on topic, we need to be very careful in genetically engineering something that nature has engineered naturally.

Responding to a comment apparently lost in a TypePad crash...

... if we are to grow our own fuel (of which I am not convinced that we can ever do), we need to use a naturally growing plant, and not introduce some genetically derived plant to replace what grows naturally.
Well, that excludes corn.  And wheat.  And just about any crop that mankind has grown for food for very long; we've selectively bred these plants for longer than recorded history, and deliberately mutated them to create new traits for quite some time.  Splicing specific genes is just a faster and more efficient way of doing what we (and arguably some other organisms, like plant viruses) have been doing since the dawn of agriculture.
An early attempt to use GMO's to breakdown cellulose into ethanol created a bacteria that caused plants to die when the left over mash was applied to the soil.
Oh, really?  What was this organism, and how did a modification in a cellulase enzyme (which a great many decomposers have) turn the GMO poisonous?  Got a cite, or is this just some urban folklore?
What if we are too successful at creating a prolific species of switchgrass that spreads like dandilions?
If switchgrass could have done that, it would have done it naturally a long time ago.  GM alterations would probably be aimed toward making it easier to process into fuel, or fixing its own nitrogen.  Both would make it easier for certain bugs to eat, too.

Actually, if a patented GM plant seed lands and grows on your land, you can and most likely will be sued for patent infringement. The threat of GM plant pollution is real, both on a biodiversity level and within the legal games framework. I think transgenic organisms should be kept under close guard, within labs, greenhouses, etc... But it's a bit late in most cases, we've started a big 'ol global genetic experiment, other much more cautious nations are watching the side effects closely.

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