Project Info

Who are we?

The Eli and Edythe L. Broad Institute is a partnership among MIT, Harvard and affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.

The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

What is the project?

Mission
We have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome.

Sequence and Assembly
During the initial, or shotgun phase, of a WGS project we sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy (> 10X) assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Our approach toward the initial assembly was conservative, meaning that we would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, our initial assembly (version 1) contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together.

After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus.

These two phases resulted in our first assembly (version 1) created February 2001.

During third phase we end sequenced cosmid and BAC libraries and added these reads to the assembly data in order to create a new assembly (version 2) in August 2001. The three libraries are:

  • BAC
  • Cosmid pLORIST
  • Cosmid pMOcosX
We have displayed the addresses of those clones that have both of their ends unambiguously placed in our assembly. Using the addresses provided, researchers may request the clones from the Fungal Genetics Stock Center to obtain clones corresponding to specific regions of the genome.

Genome analysis publication

After the automated annotation was performed and released to the public, the Broad Institute initiated a Community Analysis Project to study to Neurospora crassa genome in close collaboration with over 30 members of the Neurospora research community.

This collaboration resulted in the publication of:

The genome sequence of the filamentous fungus Neurospora crassa James E. Galagan, Sarah E. Calvo, Katherine A. Borkovich, Eric U. Selker, Nick D. Read, David Jaffe, William Fitzhugh, Li-Jun Ma, Serge Smirnov, Seth Purcell, Bushra Rehman, Timothy Elkins, Reinhard Engels, Shunguang Wang, Cydney B. Nielsen, Jonathan Butler, Matthew Endrizzi, Dayong Qui, Peter Ianakiev, Deborah Bell-Pedersen, Mary Anne Nelson, Margaret Werner-Washburne, Claude P. Selitrennikoff, John A. Kinsey, Edward L. Braun, Alex Zelter, Ulrich Schulte, Gregory O. Kothe, Gregory Jedd, Werner Mewes, Chuck Staben, Edward Marcotte, David Greenberg, Alice Roy, Karen Foley, Jerome Naylor, Nicole Stange-Thomann, Robert Barrett, Sante Gnerre, Michael Kamal, Manolis Kamvysselis, Evan Mauceli, Cord Bielke, Stephen Rudd, Dmitrij Frishman, Svetlana Krystofova, Carolyn Rasmussen, Robert L. Metzenberg, David D. Perkins, Scott Kroken, Carlo Cogoni, Giuseppe Macino, David Catcheside, Weixi Li, Robert J. Pratt, Stephen A. Osmani, Colin P. C. Desouza, Louise Glass, Marc J. Orbach, J. Andrew Berglund, Rodger Voelker, Oded Yarden, Michael Plamann, Stephan Seiler, Jay Dunlap, Alan Radford, Rodolfo Aramayo, Donald O. Natvig, Lisa A. Alex, Gertrud Mannhaupt, Daniel J. Ebbole, Michael Freitag, Ian Paulsen, Matthew S. Sachs, Eric S. Lander, Chad Nusbaum & Bruce Birren. Nature 422, 859 - 868 (2003)

Photo Credits

The lovely Neurospora crassa electron micrographs are courtesy of Matt Springer, Stanford University, and the Fungal Genetics Stock Center, and Dr. Namboori B. Raju of Stanford University.