First Tree Genome Sequenced

Environment & Ecology / by Virginia Hughes /

Finding could lead to next biofuel source.

tree_genome2.jpg Credit: Science

Five months after the completion of the human genome, a group of scientists representing 34 institutions around the world has published the first complete DNA sequence of a tree. As well as detailing the evolution of the poplar tree, the sequence may provide the first step in using the plant as a renewable feedstock for a “biofuel” that might one day replace gasoline.

The cell walls of the tall, fast-growing Populus trichocarpa are made up of the carbohydrate cellulose, which can be chemically converted into ethanol, a popular biofuel already in use with newer “flex-fuel” vehicles. 

“With the entire genome of the tree, we can create a holistic picture of how cellulose is produced and learn how to tweak that process,” said molecular ecologist Stephen DiFazio, one of the authors of the new study, published in the Sept. 15 issue of Science

DiFazio envisions a future of tree crops that have been selectively bred to have shorter generations and produce cellulose more efficiently, just like the super-productive corn or rice plots of today.

“A lot of the fallow land in the U.S. could be highly productive tree plantations,” he said.

“It’s a keystone species for a lot of ecosystems in the U.S.,” he continued, adding that in many dry regions in the western United States, the poplar is the only tree species.

Since poplar trees naturally absorb carbon dioxide from the air and funnel it to their roots and the surrounding soil, some scientists say that a fuel made from tree crops could be carbon neutral. At the very least, it would yield far lower levels of greenhouse gases than fossil fuels.

Prior to this study, only two plants had been fully sequenced—in 2000, a tiny weed known as Arabidopsis thaliana, and rice in 2004.

Because it matures in as fast as four years and has a relatively small genome—it’s only about one-sixth the size of the human genome and 40 times smaller than genome of the pine tree—Populus was an ideal choice for gene sequencing, said Difazio. His team used the “shotgun sequencing” technique in order to decode the genome, which involves cutting the genome into small, easily sequenced bits, and then reassembling them in a computer in order to infer the complete sequence.

Once sequenced, the tree genome revealed a few surprises to the researchers: It has twice as many protein-encoding genes as the human genome, and compared to the weed Arabidopsis, the poplar has more genes involved in disease resistance and wood formation.

The researchers involved, who were led by DOE scientist Gerald Tuskan, predict that current science is at least 10 years from breeding poplars that would efficiently produce the right kind of cellulose for biofuel. DiFazio notes that some of that delay will likely be due to government regulations and public approval.

“There’s a misconception that we’re going to be replacing native, diverse, and aesthetically-pleasing forests with ‘Frankentree’ plantations,” he said. “That’s really not the case. We’re talking about an agricultural model.”

Jim McMillan, manager of biorefining process research at the National Renewable Energy Laboratory contends that the completed poplar sequence “[is] only one step of many that needs to happen” for trees to become major players in the budding biofuel industry.

All of the ethanol currently made in the U.S. comes from corn, said David Thomassen, chief scientist in the office of biological and environmental research at the Department of Energy, which led the study along with the Oak Ridge National Laboratory.

“Even if we used all the corn crop that’s produced every year in the U.S., there wouldn’t be enough,” he said, noting that we’d even fall short of the Bush administration’s goal of a 30 percent reduction in oil use by 2030.

Thomassen added that the environmental problems of energy and climate change won’t be solved with the study of just one tree; the poplar, after all, isn’t the only plant capable of producing ethanol.

“We need a variety of cost-effective and plentiful feedstocks,” he said, “and a broader understanding of how to use biology to produce ethanol.”

Originally published September 14, 2006

Tags ecology energy research

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