With an estimated 1.5 million species, fungi represent one of the largest branches of the Tree of Life. They have an enormous impact on human affairs and ecosystem functioning due to their diverse activities as decomposers and pathogens, and their partnership with host organisms for mutual benefit. To use fungi for the benefit of humankind, an accurate understanding of what exactly they do, how they function, and how they interact in natural and synthetic environments is required.
Jason Stajich, an assistant professor of plant pathology and microbiology at the University of California, Riverside, is a member of an international research team that, in collaboration with the Joint Genome Institute of the U.S. Department of Energy, has embarked on a five-year project to sequence 1000 fungal genomes from across the Fungal Tree of Life.
Called the “1000 Fungal Genomes” project, the research endeavor aims to bridge the gap in our understanding of fungal diversity and is one of 41 projects funded through the U.S. Department of Energy’s 2012 Community Sequencing Program.
“The overall plan is to fill in gaps in the Fungal Tree of Life by sequencing at least two species from every known fungal family,” said Stajich, a member of UCR’s Institute for Integrative Genome Biology. “Once the data is compiled, the project scientists will make use of the data as a starting point for interpreting how these organisms change and use their environment to make a living.”
Stajich is co-leading the Fungal Genomes project with Joey Spatafora, a professor of botany and plant pathology at Oregon State University. Along with a team of collaborators, their labs will coordinate the selection of fungal strains to analyze the data to answer questions about the evolution of fungi across the fungi kingdom, the evolutionary relatedness among the fungi, and their gene content.
Essential biological components of the global carbon cycle, fungi break down dead organic material. Collectively, they are capable of degrading almost any naturally occurring biopolymer and numerous human-made ones. Fungi hold considerable promise in the development of alternative fuels, carbon sequestration and bioremediation of contaminated ecosystems. They are important, too, in the production of drugs, chocolate, beer and some cheeses. To date, however, only about 100,000 species of fungi have been named.
“The ability to sample environments for complex communities by sequencing genomic DNA is rapidly becoming a reality and will play an important part in harnessing fungi for industrial, energy and climate management purposes,” Stajich said. “However, our ability to accurately analyze these data relies on well-characterized, foundational reference data of fungal genomes.”
At least five stock centers – the Fungal Genetics Stock Center, University of Missouri, Kansas City; the Robert L. Gilbertson Mycological Herbarium, the University of Arizona; Centraalbureau voor Schimmelcultures Fungal Biodiversiry Centre, the Netherlands; the U.S. Department of Agriculture Northern Regional Research Laboratory; and the U.S. Department of Agriculture Center for Forest Mycology Research – will provide the fungal species for analysis.
Stajich also will be involved in two other proposals funded by the Department of Energy’s Joint Genome Institute:
The thermophilic fungi project: The research team, led by scientists at Sandia National Laboratories, will seek to explore the molecular basis of the evolution of “thermophily,” the ability of an organism to grow at a high temperature, in two groups of fungi which, in the long run, could help in developing new thermostable enzymes for industrial applications.
The Coprinopsis cinerea project: Researchers, led by scientists at the University of North Carolina at Chapel Hill, will work to understand how the model mushroom Coprinopsis cinerea degrades biomass, and profile its development to explore, ultimately, “how to build a mushroom.”
“I will explore the role of natural selection and changes in the copy numbers of repetitive elements called transposons to understand how thermophillic fungi have acquired their ability to grow at high temperatures,” Stajich said. “For the Coprinopsis project I will help catalog genes and study how these genes are regulated.”