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 Black cottonwood. Photo by Dave Powell, USDA Forest Service www.forestryimages.org |
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Southern Research Station Scientists Help Sequence Poplar Genome
Asheville,NC -- On September 15, 2006, an international team of scientists announced the first complete DNA sequence of a tree, the black cottonwood (Populus trichocarpa). Black cottonwood is a member of the poplar family, which holds great promise as a feedstock for new biofuels, and is already used to create buffers and restore riparian areas.
The research is the result of a four-year scientific and technical effort led by the U.S. Department of EnergyÂs Joint Genome Institute and Oak Ridge National Laboratory, uniting the efforts of 34 institutions around the world - including the SRS Southern Institute of Forest Genetics (SIFG) based in Saucier, MS.
SIFG project leader and research geneticist C. Dana Nelson and research geneticist Nurul Islam-Faridi are co-authors of the Science article that announced the sequencing and assembly of the cottonwood genome. Faridi, who also leads the Forest Tree Molecular Cytogenetics Laboratory at Texas A&M University, contributed cytogenetics studies that helped the team reassemble the genome and begin to locate genes of both evolutionary interest and economic importance
The poplar genome was sequenced using the "shotgun" method. The DNA molecule is broken into small fragments which are then sequenced separately. A computer program finds sections of matching sequences that are then used to patch the genome back together on "scaffolds" that represent chromosomes. One of the problems with this method is that, like the genomes of most species, the poplar genome contains significant repetitive sequences that, when cut up, can be put back together in more than one way.
Since poplar has only 19 chromosomes, in theory there should be as few as 19 scaffolds, stretches of genome reassembled by overlapping end sequences. At one time in the poplar project, researchers had assembled 2447 scaffolds. Faridi uses a technique called fluorescence in situ hybridization (FISH) to physically locate and validate the positions of major repetitive DNA sequences on the poplar chromosomes.
"Getting this alignment right is essential for completing the sequencing of the genome," says Nelson. "It will also allow us to map and eventually clone economically and ecologically important genes."
In addition, Faridi and Nelson generated and analyzed data to provide an estimate of the amount of functional DNA within the genome, an important parameter in validating the evolutionary history of the genus.
Next steps include additional FISH work to assign and position as many scaffolds as possible to the 19 chromosomes and to utilize the P. trichocarpa genome information within the cottonwood species native to the southern United States (P. deltoides) to improve traits for biomass production and riparian zone restoration.
For more information:
C. Dana Nelson at 228-832-2747 x201 or
dananelson@fs.fed.us
Nurul Faridi at 979-862-3908 or
nfaridi@fs.fed.us
Read more about the project in the Science news article: http://www.sciencemag.org/cgi/content/full/313/5793/1556a
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