Whitehead Institute Receives National Science Foundation Grant to Sequence Neurospora

CAMBRIDGE, Mass. — The Whitehead Institute for Biomedical Research has received a two-year, $5.25 million grant from the National Science Foundation to sequence the genome of the common laboratory fungus Neurospora crassa and to deposit the information in public databases.

The Whitehead researchers, with collaborators at the Oregon Graduate Institute of Science and Technology, the University of Kentucky and the Fungal Genetics Stock Center, will also initiate the annotation of the sequence – the identification of genes and other important features of the genome – and develop tools to display the information in ways that will be useful to the research communities. The Neurospora genome consists of 43 million base pairs, or DNA letters.

Like the fruit fly, Neurospora has long served as a powerful laboratory model to study genetics and biological mechanisms. In fact, it was with Neurospora that scientists first demonstrated the concept that one gene makes one corresponding protein. The ease of growth and the extensive genetic tools available for Neurospora make it a convenient system for the study of many processes found in higher organisms. It is the most intensively investigated member of the filamentous fungi, a group of organisms that are more complex than yeasts, and that are of profound significance to human health and welfare.

"As a result, sequencing the Neurospora genome is an important goal for biomedical research," says Bruce Birren, Assistant Director of the Whitehead Institute sequencing center and leader of this project. "Just as the genome sequences of the yeast, worm, fruit fly, and the human have helped accelerate biomedical research, sequencing this fungus will provide many new insights into life’s processes."

"As the largest contributor to the human genome project, the Whitehead Institute Center for Genome Research is uniquely poised to take on this task," says Eric Lander, Director of the Center. "We hope to apply the genomic tools we’ve developed to sequence the human genome to rapidly decipher the sequence of Neurospora."

"Many labs around the world are eager to exploit this sequence information and carry out exciting biology, but they lack the resources and expertise needed to efficiently sequence the genome. Making the Neurospora genome sequence available in the public databases and developing new approaches to analysis of the sequence will accelerate research in many areas," says Birren.

Another important outcome of Neurospora sequencing will be its contribution to the growing field of comparative genomics. Because many important genes are conserved among species, finding genes in one organism will help shed light on analogous genes in other organisms (including humans). Comparing the DNA sequences of various organisms will also help researchers understand the key genes and genetic mechanisms that have been conserved throughout evolution.

DNA sequencing, which is determining the exact order of the four possible chemical bases, commonly abbreviated A, T, C and G, has been greatly expedited by recent technological advances, some of which were developed at the Whitehead Institute Center for Genome Research.

The Whitehead's sequencing center is a high-throughput production facility for genome sequencing. It has 12 custom-made, factory-style robotic systems and 158 capillary-based DNA sequencers that crank out some 135,000 sequencing reactions per day – translating to 42 million sequencing reactions per year. This output makes the center the largest of the publicly funded sequencing centers.

"We have achieved this by inventing methods that are easily scaled and by automating laboratory robotics and informatics systems. Our goal is to use our experience in managing large scale projects, our experience in developing efficient methods for finishing, and our close ties with the Neurospora research community to rapidly produce finished sequence for the Neurospora genome," says Birren.