Issue 8

Improving Buffer Trees: The Poplar Genome Sequenced

On September 15, 2006, an international team of scientists announced the first complete genome sequence of a tree, the black cottonwood. Black cottonwood is a member of the poplar family, which is widely used to create buffers and restore riparian areas. The research is the result of a 4-year scientific and technical effort led by the U.S. Department of Energy’s Joint Genome Institute and Oak Ridge National Laboratory that united the efforts of 34 institutions—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 were coauthors of the Science article that announced the sequencing and assembly of the cottonwood genome. Faridi, who also leads the Forest Tree Molecular Cytogenics Laboratory at Texas A&M University, contributed the studies of chromosome structure that helped the team to 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 researchers use to patch the genome back together on “scaffolds” that represent the chromosomes. One of the problems with this method is that, like the genomes of most species, the poplar genome contains significant repetitive sequences, what used to be called “junk DNA.” When these repetitive sequences are cut up, they can be put back together in more than one way.

Since poplar has only 19 chromosomes, in theory there should be 19 scaffolds, but at one point in the poplar project, researchers had assembled 2,447 possible scaffolds. Faridi’s first task was to physically locate and validate the positions of major repetitive DNA sequences on the poplar chromosomes. The next step is to assign and position as many scaffolds as possible to the 19 chromosomes.

Ultimately, this information will be used to further improve the traits in poplars that already make them so important for buffers and riparian zone restoration projects. —ZH

For more information:
Dana Nelson at 228–832–2747, x201 or dananelson@fs.fed.us.
Nurul Faridi at 979–862–3908 or nfaridi@fs.fed.us.

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