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Keys to the Kingdom

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Genomic research of fungi reveals the secrets behind penicillin and pale ale

Although fungi belong to one of the world’s most diverse kingdoms, we know relatively little about them. That’s about to change.

Using powerful new tools of genomics, Joseph Spatafora and an international team of scientists will sequence the full set of chromosomes for 1,000 fungus species, creating at least two reference genomes for each recognized family within the fungal kingdom.

“With this genome encyclopedia we’ll have access to the playbook of fungi,” Spatafora said, a playbook that includes insights into carbon cycling, food science, environmental clean up, human health, and more.

The project will decode some of the rock stars of the fungus kingdom, including the Armillaria fungus that extends its filaments among tree roots across more than three square miles, making it one of Earth’s largest organisms. The project will decode heat-loving fungi that thrive in the geysers of Yellowstone; and fungi found only in Arctic ice; and hardworking fungi that produce life-saving pharmaceuticals such as penicillin, cholesterol-lowering statins, and the immunosuppressant cyclosporins, which made organ transplants possible.

Fungi have an enormous impact on life and ecosystem functioning, as decomposers, pathogens, and essential components of the global carbon cycle. They are capable of degrading almost any biological material as well as many synthetic compounds. They are key ingredients in the development of alternative fuels, carbon sequestration, and bioremediation of polluted sites. Fungi have even been recruited in the war against drugs to eradicate coca plantations and heroin poppies.

“We’ve used fungi for so many services to society for centuries without much knowledge about how they are assembled at a genomic level. Think about what we can discover with this powerful new knowledge,” he said.

Joseph Spatafora
Joseph Spatafora, an OSU professor of botany and plant pathology, uses an extensive computer system to manage the enormous amount of data generated as he and his international team sequence the full set of chromosomes for 1,000 fungus species. Photo by Lynn Ketchum.

Once thought to be plants, fungi are now recognized as their own kingdom and are actually more closely related to animals than they are plants. There are an estimated 1.5 million species of fungi, yet only about 100,000 species have been described. Spatafora credits recent advances in gene sequencing technology that will make it possible to unravel genetic details with speed and accuracy.

Just as we’ve witnessed information storage shrinking to terabytes in a thumb drive, new genomics technologies make it possible to scan millions of strands of DNA in parallel and to deliver orders of magnitude more information many times faster than ever before.

What happens to all those numbers?

“This deluge of data requires new tools for computation that allow us to mine enormous datasets of genomic information,” Spatafora said. “With these new tools, we can pursue biologically relevant questions such as the evolution of carbohydrate metabolism.” Spatafora credits these advancements in computational biology to collaborations with researchers associated with the OSU Center for Genome Research and Biocomputing, which houses an internationally recognized state-of-the-art computational infrastructure.

The 1000 Fungal Genomes project builds on the knowledge created by a previous 10-year study called Assembling the Fungal Tree of Life, also led by Spatafora. That study helped to develop a classification system of fungi from around the world. But mapping out a family tree is only the starting point in understanding how an organism functions in nature. To understand the full potential of a fungus, scientists sequence genes that are directly involved in its metabolism. From there, they can better understand the role of that organism in the processes that keep life running on earth.

This project is one of 41 projects funded through the U.S. Department of Energy’s Joint Genome Institute, whose purpose is to enable scientists from universities and national laboratories around the world to explore the hidden world of microbes and plants for solutions to major challenges in energy, climate, and environment.

Spatafora collaborates with an international team of researchers, including Jason Stajich at University of California at Riverside and Igor Grigoriev of the U.S. Department of Energy Joint Genome Institute.

For more information, see the 1000 Fungal Genomes Project website.

Published in: Innovations