WALNUT CREEK, CA–Despite the perception that the genetic diversity among animals–ranging from humans to worms–is enormous, the reality is that it pales in comparison to the diversity between the microbes that make up the bulk of the biomass on the planet.
Accordingly, to close conspicuous gaps in our understanding of the tree of life, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) announces a heavy emphasis on microbes making up the list of organisms that will stoke the DNA sequencing engine of its Community Sequencing Program (CSP) over the coming year.
“The CSP selections represent a rich collection of microorganisms as well as higher plants and animals that inhabit both aquatic and terrestrial ecosystems,” says Eddy Rubin, JGI Director. “By making JGI’s powerful resources available to non-traditional end-users of sequence through the CSP we hope to advance knowledge across such vital topics as alternative energy production and bioremediation, and to address important questions of evolution and development.”
Supported by the DOE’s Office of Science, the CSP will allocate roughly15 gigabases (billions of letters of genetic code) of sequencing–roughly 50 percent of JGI’s total capacity–for the 23 projects selected from nearly 60 submitted earlier this year.
Among the larger organisms queuing up at the 100 sequencers at JGI’s Production Genomics Facility is the moss Physcomitrella patens, which has a genome size of just over half a billion bases. “Physcomitrella is a wonderful model system in that it is small, grows quickly, and is very amenable to comparative studies,” says Brent D. Mishler, Director, University & Jepson Herbaria, and Professor of Integrative Biology, University of California, Berkeley. “Human comparative genomics has benefited from having a series of genome projects along the tree of life–mouse, puffer fish, fruit fly, worm–while plant genomics has suffered since only a closely related cluster of cereals and the mustard Arabidopsis have been sequenced. This will be a triumph for international plant science.”
Mosses were among the first plants to colonize the land, 450 million years ago. They pre-date the flowering plants by some 200 million years of evolutionary time. “Mosses can do many of the things that the flowering plants have forgotten,” says Mishler. “Some of their primitive traits–like the ability to survive extremes of dehydration–would be useful to incorporate in modern-day crops, especially in less developed countries. By studying the genes that control these traits in the moss, we should be able to identify how these characteristics could be revived in flowering plants.”
Adding to the JGI’s leadership in plant genomics will be Selaginella moellendorffii, or the Gemmiferous Spike Moss. Selaginella and Physcomitrella will be the first nonflowering vascular plants to be sequenced.
“The Selaginella sequence will lead us down the evolutionary path toward such traits as those that allow plants to survive and thrive on dry land,” says Jo Ann Banks, Professor of Botany at Purdue University. “It will also enable us to identify proteins, metabolites, or small molecules produced by this plant that may be beneficial for human health and agriculture.”
JGI’s sequencing will also target several animals selected to fill critical gaps in the tree of life. One will be the leech Helobdella, long used as a model system by biologists studying embryological development and functions of the nervous system. Along with the polychaete worm, Capitella, and the mollusk Lottia, also selected, these are expected to be the first representatives sequenced from the large animal group dubbed the Lophotrochozoa. This group, comprising about one third of all animal phyla, promises to reveal many of life’s processes and to exemplify intermediate features underlying the patterns of genome evolution. Early branches of the tree of life will be represented by the sponge Reniera and an odd organism called Trichoplax adhaerens. With a superficial resemblance to a giant amoeba, Trichoplax has the smallest animal genome, less than 50 million base pairs.
Other organisms in the CSP queue include the cold water-dwelling microbes, Crenarchaeota, which offer another important foray into environmental genomics, according to project leader Edward DeLong of the Massachusetts Institute of Technology. “These Crenarchaeota have not yet been cultivated, so their biological properties are not well known. Oceanographers are particularly interested in how these microbes may be involved in the carbon and energy cycles of the deep sea.” Crenarchaeota are members of the Archaea, a major branch of life that includes many microbial extremophiles–microbes that can live at extreme temperature, salinity, or high acidity.
Additional CSP DNA sequencing projects in the pipeline include the following:
- The complex bacterial community that lives under the skin of the gutless marine worm Olavius algarvensis and provide the energy source for the host.
- Staphylococcus aureus, a food-borne pathogen that is implicated in thousands of infections in the U.S. alone. Sequencing of an antibiotic resistant form of this organism will inform how antibiotic resistance occurs.
- Sequencing of groundwater samples from contaminated sites within the Oak Ridge National Laboratory Y12 Security Complex. The site contains one of the highest-concentration plumes of mobile uranium along with volatile organics, technetium, nitrate, aluminum, thorium, zinc, and nickel. Sequences generated will complement biogeochemistry, hydrology, microbiology, and engineering studies to help evaluate the impacts of contaminants and remediation treatments on microbial community dynamics.
- Karenia brevis, a single-celled alga responsible for the natural saltwater phenomenon known as “red tide,” which can pose a human health risk and detrimentally affect regional marine economies.
- Accumulibacter phosphatis stores huge amounts of phosphorus inside its cell. Engineers have exploited this capability to remove excess phosphorus–initially from fertilizers and detergents–from wastewater. Too much phosphorous can over-stimulate microbial growth, resulting in eutrophication, where oxygen in the water is depleted and fish and other organisms residing in the habitat die.
- Alvinella pompejana, the marine Pompeii worm, which has adapted to thrive at super-hot hydrothermal vents.
- Prochlorococcus, a marine phytoplankton that plays a critical role in regulating the dynamics of the global carbon cycle, responsible for a significant fraction of photosynthesis in the world’s oceans.
- Lactobacillus rhamnosus is considered a potential probiotic, which can protect its host and prevent disease.
“These projects were the result of a rigorous competitive call for proposals vetted by an external scientific review panel. The successful applications represent terrific science that will advance our understanding of the natural world,” says Rubin. As with all other sequencing projects at JGI, data generated will be made freely available to the entire scientific community.
The Joint Genome Institute was established in 1997 as part of the Human Genome Project by combining the DNA sequencing resources from the three DOE national laboratories managed by the University of California: Lawrence Berkeley and Lawrence Livermore national laboratories in California, and Los Alamos National Laboratory in New Mexico. JGI has since extended the scope of its sequencing to whole-genome projects devoted to microbes and microbial communities, model system vertebrates, aquatic organisms, and plants. Funding for the JGI is predominantly from the Office of Biological and Environmental Research in the DOE Office of Science.