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JGI Unveils 2009 Genomic and Metagenomic Sequencing Plans

NEW YORK (GenomeWeb News) – The DOE’s Joint Genome Institute today named 44 genomic sequencing projects that its Community Sequencing Program will support in 2009 to find information it can use in new biomass and bioenergy programs.
Researchers will explore a wide variety of sources — including the guts of an Amazonian stinkbird, a wood-boring marine bivalve, the surfaces of ponds, and the forests of the southern US — for genomic and metagenomic information they can use to develop renewable and clean energy strategies.
"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," JGI Director Eddy Rubin said in a statement.
"The range of projects spans important terrestrial contributors to biomass production in the Loblolly pine — the cornerstone of the US forest products industry — to phytoplankton, barely visible to the naked eye, but no less important to the massive generation of fixed carbon in our marine ecosystems," Rubin added.
In one project, Mississippi State University’s Daniel Peterson will look at the Loblolly’s genome for genes that could be used for molecular programs to improve the pine as a source of biomass feedstock, as a carbon sequestration tool, and as a source of raw materials.
Researchers also will study the genes of marine microbes called nanoflagellates, which eat other microbes such as bacteria and phytoplankton. The Monterey Bay Aquarium Research Institute’s Alexandra Worden will study the genetic mechanisms involved in nanoflagellate predation, digestion, and biomass incorporation of the phytoplankton and bacteria.
The CSP scientists also will study Spirodela polyrhiza, or greater duckweed, which is the “smallest, fastest growing, and simplest of flowering plants,” according to JGI.
"These plants produce 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," said Rubin. "Moreover, duckweed relates to all three of DOE JGI's mission areas: bioenergy, bioremediation, and global carbon cycling."
This sequencing project was submitted to the CSP by Todd Michael of the Waksman Institute of Microbiology at Rutgers, the State University of New Jersey, and will involve six institutions.
Among the metagenomic sequencing programs being undertaken is research proposed by Daniel Distel of the Ocean Genome Legacy Foundation, who will study how the Pacific shipworm, a marine bivalve, can survive on a diet of wood. Although they have been called “termites of the sea,” these shipworms have a system for degrading lignocellulose that is “biologically, functionally, and evolutionarily distinct from those found in termites,” JGI said, and that allows them to accomplish the task with “just a few related types of microbes.”
Another marine project, led by Andrew Koppisch and others at Los Alamos National Laboratory, will focus on a colony-forming green microalga called Botryococcus braunii that could provide metabolic pathways responsible for hydrocarbon synthesis that could be used in producing biofuels.
Another metagenomics project involves studying the foregut of a pheasant-like stinkbird called the hoatzin.
The hoatzin has an enlargement in its esophagus that “harbors an impressive array of novel microbes,” JGI said. Studying the contents of this organ could lead to the discovery of microbial enzymes that could degrade plant cell walls.
A full list of the DOE JGI’s planned 2009 sequencing projects can be found here.

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