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Chuck Staben & Mark Farman
Analyzing Fungal Genomes

by Jeff Worley & Robin Roenker

Telomeres are the end sections of chromosomes, composed of repetitive sequences of DNA traditionally viewed merely as inconsequential placeholders within the larger genome. Typically, scientists working to analyze and assemble genomes of various organisms have omitted the telomeres entirely from their results.

Photo of Chuck Staben (left) and Mark FarmanIn doing so, however, the researchers may be disregarding vital genes located in what's known as the chromosome's subtelomeric region—genes that could be responsible for specialized processes that allow that organism to adapt and live in its particular environmental niche.

At least that's the stance taken by Chuck Staben, associate vice president for research and an associate professor of biology, and Mark Farman, associate professor of plant pathology, in their current research that focuses on genome analysis of fungi.

"It's a contrary view, an emergent view," says Staben, who came to UK in 1989. "But it turns out that there is a tremendous amount of biological variability at the ends of the chromosomes, and that variability relates to whether or not that particular fungus can, say, infect a plant or a human, or live in a particular niche."

The role of telomeres in such "niche adaptation" has been the focus of four years of research collaboration for Staben and Farman. Their preliminary findings have suggested that genes located at the telomeres are distinctive and may be responsible, for example, for allowing a particular rice blast fungus to infect only certain strains of rice or for allowing a wild strain of Saccharomyces fungus, commonly known as yeast, to ferment only specific types of sugars—such as from grapes or other compounds.

To date, Staben and Farman have analyzed and sequenced the telomeres of six different fungi, utilizing parallelized computing capacity and a specialized computer program they've designed that mines freely available national genome research databases for data on telomeres. With these tools, the researchers are able to computationally gather, reassemble and analyze telomere sequences that were previously identified but omitted from the fungal genomes because other researchers deemed them insignificant.

For telomeres that have not previously been sequenced, Staben and Farman also conduct gene sequence comparisons with the help of a program called BLAST, run on a supercomputer, in order to identify the genes located at the telomeres. And as a campus-wide service, the pair routinely run requested gene sequence comparisons via their "BLAST server" for other UK researchers.

While Staben and Farman's work focuses on fungal genome analysis, they believe their hypothesis about the significance of telomeres in niche adaptation may hold true for other, more complex organisms as well.

"We hope that our computational research will be able to guide biological experiments that other researchers might want to do," Staben says. "Our focus has been on identifying these interesting genes at the edge of these telomeres. Other researchers can then follow up on that to conduct experiments, modifying those genes or clipping off that part of the chromosome, to determine how those changes affect the organism's niche adaptation."

About Chuck Staben and Mark Farman

Chuck Staben and Mark Farman have collaborated on their fungal genome research project for the past four years. It was Farman who initially proposed their development of laboratory methods to sequence telomeres, Staben says, "because he recognized that no one else was doing it, and he thought it was important." So far, the pair has sequenced the telomeres of six fungi.

Staben and Farman Research Team

Weixi Li, UK doctoral student in biology