Whitehead Genome Center Scientists Assemble Draft Sequence of Ustilago maydis

September 23, 2003

Tags: Genetics + Genomics

CAMBRIDGE, Mass. — Scientists at the Whitehead Institute/MIT Center for Genome Research (WICGR) have publicly released a high quality draft genome sequence of Ustilago maydis, commonly known as corn smut, an important model system for the study of plant fungal diseases. In the United States, U. maydis poses a significant economic threat to agriculture. In Mexico, U. maydis or “huitlacoche,” is a culinary delicacy. The U. maydis sequence is freely available at http://www-genome.wi.mit.edu/annotation/fungi/ustilago_maydis/index.html.

U. maydis is a fungus that primarily attacks sweet corn plants. Infected kernels grow large and oddly shaped, turning grey or black as they fill with spores. The disease stunts plant growth and reduces crop yield. U. maydis is responsible for severe economic losses in agriculture worldwide, causing billions of dollars of damage every year to corn, one of the world's major cereal crops.

“Instead of observing one gene at a time, it will now be possible to observe more than 6,000 genes simultaneously,” says Scott Gold, Associate Professor of Plant Pathology at the University of Georgia. “The U. maydis genome sequence will allow scientists to more rapidly determine the genes involved in causing disease.”

U. maydis is one of the leading model systems for study of fungal plant pathogens. It can be cultured easily on both young corn plants and synthetic media, and is an excellent model system to study pathogen and host interaction. U. maydis is also a critical model organism for genetics and cell biology. The DNA recombinant structure Holliday junction was first observed in this species.

Farmers in the United States destroy the fungus or feed it to the pigs. In Mexico, smut invading sweet corn “huitlacoche” has been prepared in Mesoamerican meals since the pre-Columbus period. The delicacy has started to appear on restaurant menus and is becoming a popular dish in “nouveau cuisine.”

The genome sequence was assembled at the Whitehead Institute/MIT Center for Genome Research, in collaboration with Bayer CropScience (BCS) and Exelixis Inc. With support from the National Human Genome Research Institute, WICGR generated 10X coverage of U. maydis. In addition, Bayer CropScience contributed 2X coverage of the genome sequence that was used as a physical map and anchor for the WICGR assembly. Exelixis Inc. provided 5X whole-genome shotgun sequences of U. maydis from a varying strain that will be used to identify polymorphisms.

The U. maydis genome is approximately 20 million base pairs in size. The draft sequence shows the order of the DNA chemical bases A, T, C, and G along the fungus’ 23 chromosomes. It includes more than 98 percent of the genome with long, continuous stretches of overlapping DNA and represents 10-fold coverage of the genome. This means that the location of every base, or DNA letter, in the U. maydis genome was determined an average of 10 times, a frequency that ensures a high degree of accuracy.

Currently, approximately 40 laboratories worldwide focus on the genetics and molecular biology of U. maydis. Nine of these laboratories—representing the United States, Australia, England, France, and Germany—are members of the Fungal Genome Initiative steering group to promote sequencing and annotation of the U. maydis genome.

The Whitehead Institute/MIT Center for Genome Research is an international leader in the field of genomics, the study of all of the genes in an organism and how they function together in health and disease. A flagship of the Human Genome Project, the Center today houses a broad range of thriving research programs combining structural genomics, medical and population genetics, and clinical medicine. The Center's annual budget is $80 million, and it employs 350 people, including scientists and medical researchers from Whitehead, MIT, and Harvard.


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