Work of Southeast Scientists Makes Cover of Worldwide Science Journal


Photo of Dr. Walt Lilly and students working in the lab

Dr. Walt Lilly, professor of biology, top, and Southeast students work in the lab to assemble the genome sequence for a mushroom called Coprinopsis cinerea.


July 6, 2010 – Years of fungal genetic research by two Southeast Missouri State University biology professors is currently featured on the cover of one of the world’s most influential science journals.

“Genome Evolution in Mushrooms” is the title of the article published in the June 30 issue of the Proceedings of the National Academy of Sciences of the United States of America. The article also features a guest commentary on the significance of the research by two scientists at the University of California Berkeley.

The journal article is the culmination of nearly six years of work by Dr. Allen Gathman and Dr. Walt Lilly, Southeast professors of biology, on the genome of the mushroom Coprinopsis cinerea.

“The paper makes a major contribution to our understanding of evolution in the phylum Basidiomycota, which includes all mushrooms as well as numerous fungal pathogens that cause disease in plants and animals, including humans,” Gathman said.  The research is important, he says, because it shows how “the organization of genes on chromosomes contributes to the functioning of the organism.”

Lilly and Gathman, along with more than a dozen Southeast students over the past six years, have worked to assemble and characterize the genome sequence for a mushroom called Coprinopsis cinerea. Their work was funded by a $744, 055 grant they received from the National Science Foundation to collaborate on research with scientists at Duke University and the University of North Carolina-Chapel Hill. The project was part of the Microbial Genome Sequencing Program of the National Science Foundation.

Gathman said the Southeast research group with their cadre of undergraduate researchers sequenced more than 6,000 gene transcripts from the organism and used those sequences to help define the structure of genes in the genome.   In addition the Southeast team performed genome-level sequencing and computational biology to close the nearly 435 gaps in the original sequence to allow for assembly of the entire 30 million DNA bases into 13 chromosomes.  

“You can think of the genome as a book, and each gene as a sentence in that book.  Those sentences are arranged into chapters, the chromosomes,” Lilly said. “Imagine starting with something like 60,000 sentence fragments and assembling those into a book with 13 chapters with interesting characters and a plot.”

Pat Pukkila, the primary investigator on the project at the University of North Carolina, has worked with Coprinopsis cinerea for many years. Lilly and Pukkila became acquainted several years ago while collaborating on a project. Pukkila was a primary proponent for getting the initial draft sequence of the Coprinus genome which was completed in 2003 by the Whitehead institute at MIT.  Pukkila coordinated the project and mapped the genes to the 13 chromosomes of Coprinopsis cinerea.    In addition, over 40 other scientists from institutions in the US, Europe and Asia contributed to the genome characterization described in the paper.

Fungi like Coprinopsis produce a large spectrum of oxidative and degradative enzymes that are of industrial interest.  Some of those enzymes may prove to be important as detergent additives, in remediation processes for contaminated soil and water, or in pharmaceutical production, Lilly says. 

Gathman says their research may be significant in controlling grain pathogens, which currently limit food production in many parts of the world. Plant pathogens such as rust and smut fungi impose major limits on the production of wheat, corn and rice, he said.

“All cereal grains have problems with basidiomycete pathogens,” he said.

“The information we came up with will help with knowing how all members of the basidiomycetes grow and function,” Gathman said. “This is a step towards understanding how this group of fungi has evolved, and how different species have adapted to specific environments.”

As a result of their work, the Southeast researchers developed and continue to maintain an interactive Coprinopsis cinerea worldwide genetics/genome database located at Southeast at http://genome/

Former Southeast students who have worked on the project over the years include 2009 graduate Hannah Korte of St. Joseph, Mo.; 2008 graduates Nathalie Pogue of St. Louis, Noriko Inoguchi of Makinohara Shizuoka, Japan, Miranda Koester of O’Fallon, Mo., and Erica Young of Valley Park, Mo; 2006 graduate Nicole Arnold of St. Louis; and 2005 graduates Sarah Wilke of Carrboro, N.C., Alex Guerrero of St. Peters, Mo., Michelle Carlson of Eden Prairie, Minn., and Amber Smith of Sikeston, Mo. Former students Bruno Murphy of Jackson, Mo., and Christian Barr of Seattle, Wash., also worked on the project. 

Lilly said the project “provided students with experience at the forefront of molecular biology.  This is as ‘cutting edge’ as students can get at any university in the country,” he said.

Southeast alumna Sarah Wilke of Carrboro, N.C., began working on the project as an undergraduate in the lab, continued as a paid lab tech, and then moved to the University of North Carolina as a lab tech under Pukkila, Gathman said.

“Sarah’s contributions were so important that she is second author on the paper,” he said.

Gathman and Lilly will continue their work in this area.  Currently they are examining changes in the expression of genes in Coprinopsis cinerea based on nutritional resources the fungus has.   They also have projects aimed at understanding one important group of enzymes produced by the fungus, those that break down proteins. Lilly said, “by comparing  proteases of Coprinopsis to other fungi that live in different environments, the importance of individual enzymes may be discovered.”   Lilly and Gathman are involved in characterizing other basidiomycete genomes as well.   The description of the genome of Schizophyllum commune, a wood decaying fungus which they have studied for decades is scheduled to be published soon.   Because it is also a basidiomycete, the gene order along chromosomes is similar. He said their earlier work with Coprinopsis cinerea will serve as a guide and make it easier in the future to assemble full chromosomes of Schizophyllum commune and other fungi.