WALNUT CREEK, CA–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).
Mimulus guttatus, the common monkey flower
“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 genomics.”
“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.
The butterfly Bicyclus anynana
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 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 is also available.
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.