DOE Joint Genome Institute details projects

By Kris Bevill | June 02, 2008
Web exclusive posted July 7, 2008 at 9:09 a.m. CST

The U.S. DOE Joint Genome Institute has announced 44 DNA sequencing projects it will undertake in the next year. Nearly 150 proposals were submitted to the DOE JGI through the Community Sequencing Program, which serves to provide the scientific community with access to high-throughput sequencing at the institute. Selected projects were chosen based on scientific merit and relevance to issues in bioenergy, global carbon cycling and bioremediation.

"The scientific and technological advances enabled by the information that we generate from these selections promise to take us faster and further down the path toward clean, renewable transportation fuels while affording us a more comprehensive understanding of the global carbon cycle," said Eddy Rubin, DOE JGI director.

Projects range from giant pine tree genomes to tiny aquatic flowering plants to complex microbial communities that are isolated from the environment or reside inside a larger organism, otherwise known as metagenomes.

The Loblolly pine is one of the most commonly planted tree species in the United States and, according to Rubin, is a cost-effective feedstock for cellulosic ethanol production. The DOE JGI plans to study the structure of the pine's genome and focus on genes that can be used for molecular breeding programs to improve the tree as a biomass feedstock, among other uses.

Another sequencing project involves the Greater Duckweed, an aquatic flowering plant that measures a miniscule 10 millimeters or less. "These plants produces biomass faster than any other flowering plant, and their carbohydrate content is readily converted to fermentable sugars by using commercially available enzymes developed for corn-based ethanol production," Rubin said.

Metagenome projects taking place in the next year include work on the giant Pacific shipworm and the Amazonian stinkbird. The shipworms, often referred to as the "termites of the sea," house a digestive system capable of symbiotic lignocellulose degradation that is distinct from any similar system found in termites, ruminants or any other cellulose-consuming animal. While similar to termites, shipworms are capable of breaking down lignocellulose with a simple intracellular consortium of just a few related types of microbes, according to the DOE JGI.

The curious creature known as the stinkbird or hoatzin is a leaf-eating pheasant-like bird that resides in the Amazon. The foregut of these birds includes an enlarged esophagus where fermentation of its food takes place, which also explains the bird's less-than-attractive sounding name. The DOE JGI believes that by characterizing the foregut contents, they will be able to identify novel microbial enzymes that help to break down plant cell walls.

Novozymes
, a world-leading enzyme production company, and Verenium Corp., a process technology company, have contributed to a DOE JGI project that is expected to aid in lowering in the cost of enzymes. The project will further research the fungi Trichoderma reesei strain Qm6a (T. reesei), which is currently being used in pilot cellulosic ethanol plants. The end result, presumably, will result in a greater understanding of the mechanisms behind enzyme secretion and will help to bridge the gap in industrial fungal enzyme production research.

To view a complete list of the 2009 sequencing projects, visit www.jgi.doe.gov/sequencing/cspseqplans2009.html.