|JGI Announces Community Sequencing
Extreme-environment microbes, antibiotic-resistant bacterium, moss, sponge, leech, and red-tide algae are among the selections
|Contact: David Gilbert, (925) 296-5643, [email protected]|
BERKELEY, 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 among 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's 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 nontraditional 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 roughly 15 gigabases (15 billion 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 of the University and Jepson Herbaria, University of California, Berkeley. "Human comparative genomics has benefited from having a series of genome projects along the tree of life mouse, pufferfish, 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 predate 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, which along with Physcomitrella will be the first nonflowering vascular plant 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 temperatures, salinity, or high acidity.
Additional CSP DNA sequencing projects in the pipeline include:
"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.