Foxtail Millet Offers Clues for Assembling the Switchgrass Genome

Science Daily

ScienceDaily (May 14, 2012) — Arranging DNA fragments into a genome sequence that scientists can interpret is a challenge often compared to assembling a puzzle, except there is no box to provide an idea of what the picture is even supposed to be. Sometimes there's guidance in the form of other publicly-available DNA sequences from related organisms that can be used to guide the assembly process, but its usefulness depends on how closely related any two sequences are to one another. For example, a reference genome might be so distantly related from the one being assembled, it would be akin to comparing a Model-T to a contemporary hybrid car.

For researchers interested in switchgrass, a perennial grass that the U.S. Department of Energy (DOE) is investigating as a prospective biofuels feedstock, assembling the plant genome poses an even more complicated puzzle than usual because it has multiple copies of its chromosomes. The DOE Joint Genome Institute (JGI), in an international partnership that includes the DOE BioEnergy Science Center (BESC) and the DOE Joint BioEnergy Institute (JBEI), two of the three DOE Bioenergy Research Centers, has sequenced plant genomes of related candidate bioenergy crops such as sorghum and the model grass Brachypodium. Both plants have been used as references for switchgrass, however sorghum last shared a common ancestor with switchgrass more than 20 million years ago while Brachypodium last shared a common ancestor with switchgrass more than 50 million years ago. The genome of a much closer switchgrass relative -- foxtail millet (Setaria italica) -- is described in the May 13, 2012 edition of Nature Biotechnology. All three genomes, along with those of other plants sequenced by the DOE JGI are publicly accessible on www.phytozome.net.

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Researchers study trees for biofuel clues

Autos.ca
October 27, 2011

Oak Ridge, Tennessee – Researchers are looking at a specific type of wood that occurs naturally in trees in an attempt to improve crops used for biofuel production.

A project at the U.S. Department of Energy’s BioEnergy Science Center is looking at tension wood, which forms naturally in hardwood trees in response to bending stress, and which is known to possess unique features that make it desirable as a bioenergy feedstock. Although individual elements of tension wood have been studied previously, the new project is the first to systematically characterize the wood and link its properties to sugar release. These plant sugars, known as cellulose, are fermented into alcohol for use as biofuel.

“There has been no integrated study of tension stress response that relates the molecular and biochemical properties of the wood to the amount of sugar that is released,” said Udaya Kalluri, a co-author on the study. “Tension wood in poplar trees has a special type of cell wall that is of interest because it is composed of more than 90 per cent cellulose, whereas wood is normally composed of 40 to 55 per cent cellulose. If you increase the cellulose in your feedstock material, then you can potentially extract more sugars as the quality of the wood has changed. Our study confirms this phenomenon.”

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Gene discovery could be biofuel’s “missing link”

Renewable Energy Magazine
Tuesday, 20 September 2011
Toby Price

A team of researchers at the US Department of Energy’s BioEnergy Science Center (BESC) have pinpointed the exact, single gene that controls ethanol production capacity in a microorganism. “This discovery could be the missing link in developing biomass crops that produce higher concentrations of ethanol at lower costs,” explained the centre in a recent press statement.

The discovery of the gene controlling ethanol production in a microorganism known as “Clostridium thermocellum” will mean that scientists can now experiment with genetically altering biomass plants to produce more ethanol.

Current methods to make ethanol from a type of biomass found in switchgrass and agricultural waste require the addition of expensive enzymes to break down the plant’s barriers that guard energy-rich sugars. Scientists, including those at BESC, have been working to develop a more streamlined approach in which tailor-made microorganisms produce their own enzymes that unlock the plant’s sugars and ferment them into ethanol in a single step. Identifying this gene is a key step towards making the first tailor-made microorganism that produces more ethanol.

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