Botanist leads international fungal genome project

Joey Spatafora's goal: 1,000 fungal genomes in five years

Fungi are master recyclers, turning waste into nutrients and providing humankind with everything from penicillin to pale ale. Although fungi are members of one of the world’s most diverse kingdoms, we know relatively little about them.

That is about to change.

Joseph Spatafora, a botanist at Oregon State University, sits in front of a computer system that will store the data that he and an international team generate as they sequence the full set of chromosomes for 1,000 fungus species. Photo by Lynn Ketchum.

Joseph Spatafora, a botanist at Oregon State University, sits in front of a computer system that will store the data that he and an international team generate as they sequence the full set of chromosomes for 1,000 fungus species. (Photo: Lynn Ketchum)

A new study headed by Joseph Spatafora, an Oregon State University professor of botany and plant pathology, will use powerful new tools of genomics to learn more about fungi. 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.

This 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 and paved the way for creating a reference encyclopedia of what fungi exist, how they are related, what they do and how they do it.

“With this genome encyclopedia we’ll have access to the playbook of fungi,” Spatafora said, adding that the playbook is important to carbon cycling, food science, environmental cleanup, human health and more.

Species Unknown

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.

“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 knowledge,” he said.

The 1000 Fungal Genomes 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 leads an international team of researchers, including Jason Stajich at University of California at Riverside and Igor Gregorlev of the DOE Joint Genome Institute.

Masters of Life

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. Therefore, fungi are useful in the development of alternative fuels, carbon sequestration and bioremediation of contaminated sites.

In order to harness this potential, the 1000 Fungal Genomes project will build a reference library as a foundation for accurate analyses of the enormous volumes of data that will be created through genomic research.

Tricholoma cf. terreum grows on a forest floor in Oregon’s Coast Range. (Photo: Lynn Ketchum)

Tricholoma cf. terreum grows on a forest floor in Oregon’s Coast Range. (Photo: Lynn Ketchum)

Fungal species to be analyzed will come from at least five science centers around the world, including University of Missouri at Kansas City; University of Arizona; USDA Center for Forest Mycology Research; USDA Northern Regional Research Laboratory; and the Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre, the Netherlands.

The first year of the five-year project focuses on some of the most diverse classes of fungi that have been studied so far in these culture collections. As the project matures and as knowledge grows, the research will expand to include questions of sampling strategy, curation of data, research and analytical protocols, training and publications.

See more information on the 1000 Fungal Genomes project.

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