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Researchers Help Sequence First Tree Genome
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OCTOBER 1, 2004 -- A team of Michigan Tech researchers has played a key role in an international effort to sequence the first tree genome.
The team was part of a consortium that has deciphered the genetic code of the black cottonwood. Black cottonwood, or Populus trichocarpa, is part of the poplar family of fast-growing, commercially useful trees, which includes quaking aspen. Chung-Jui Tsai, director of the Biotech Research Center and an associate professor of forest resources and environmental science, led the Michigan Tech effort.
Using gene amplification technology, Tsai's team fished out more than 13,000 gene fragments known as expressed sequence tags, or ESTs, that are represented throughout cottonwood's 480 million letters of genetic code. Hidden in these letters, now placed in order by the international research effort, are about 40,000 genes, which underlie all aspects of the tree's growth and behavior.
In addition to furthering basic science, determining the black cottonwoodís genetic blueprint could give scientists the tools to develop faster-growing trees, said Secretary Spencer Abraham of the Department of Energy, which provided major funding for the genome sequencing project.
Such trees could help buffer global warming by mopping up more of the greenhouse gas carbon dioxide, a process known as carbon sequestration, said Gerald Tuskan, whose team at the Oak Ridge National Laboratory lead the research effort. “This natural process suggests opportunities to further clean up the air by engineering trees so that they more effectively shuttle and store more carbon below ground in their roots and the soil.”
One pitfall among genetics researchers is EST redundancy, in which the same gene fragment is identified many times. Weeding out the redundant ESTs wastes time and resources that could be used to find other gene fragments, Tsai said.
Her team used a new method to reduce EST redundancy, and as a result, about 10 percent, or 1,300 of the ESTs they discovered were unique, having not been identified by any of the other research centers involved in the project.
Now that the project has ordered the black cottonwoodís 480 million letters of genetic code, the next step will be to take the 200,000 ESTs generated internationally and piece them together to map and identify its estimated 40,000 genes.
The Michigan Tech effort was made possible by a grant from the Michigan Life Sciences Corridor, which provided the microarray equipment used to validate ESTs.
The co-principal investigators on the project are Research Assistant Professor Scott Harding and Associate Professor Shekhar Joshi. Others involved are graduate student Priya Ranjan, Research Scientist Hongying Jiang and former postdoctoral scientist Yu-Ying Kao. Their work was published in the August issue of the journal Planta.
Several universities and national labs participated in mapping the Populus trichocarpa genome. The lead members of this international consortium are the U.S. Department of Energy, Genome Canada and the Umea Plant Science Centre in Sweden. |
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