1. Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA;
2. Department of Plant Pathology, University of California, Riverside, California 92521, USA;
3. Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA;
4. Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JH, UK;
5. Celera Genomics, Rockville, Maryland 20850, USA;
6. Department of Biology, Texas A & M University, College Station, Texas 77843, USA;
7. Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
8. Department of Cellular and Structural Biology, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA;
9. Department of Microbiology, University of Kansas Medical School, Kansas City, Kansas 66160, USA;
10. Department of Zoology, University of Florida, Gainesville, Florida 32611-8525, USA;
11. Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel;
12. Institute of Biochemistry, Heinrich Heine University, 40225 Düsseldorf, Germany;
13. Laboratory of Plant Molecular Biology, Rockefeller University, New York, New York 10021, USA;
14. Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftzentrum Weihenstephan, 85350 Freising-Weihenstephan, Germany;
15. Institute for Bioinformatics (MIPS), GSF-National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany;
16. T.H. Morgan School of Biological Sciences, University of Kentucky, Lexington, Kentucky 40506, USA;
17. The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA;
18. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20878, USA;
19. Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
20. Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA;
21. Dipartimento Biotecnologie Cellulari ed Ematologia, Universita' di Roma La Sapienza, Rome, Italy;
22. School of Biological Sciences, Flinders University, P.O. Box 2100, Adelaide, South Australia 5001;
23. Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA;
24. Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43211, USA;
25. Department of Plant Pathology, University of Arizona, Tucson, Arizona 85721, USA;
26. School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA;
27. Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA;
28. School of Biology, Leeds University, Leeds LS2 9JT, UK;
29. Department of Chemistry, California State Polytechnic University Pomona, Pomona, California 91768, USA;
30. Department of Plant Pathology and Microbiology, Texas A & M University, College Station, Texas 77843, USA;
31. Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Science University, Beaverton, Oregon 97006, USA;
32. Department of Biology, MIT, Cambridge, Massachusetts 02139, USA

Correspondence to: James E. Galagan¹Bruce Birren¹ Correspondence and requests for materials should be addressed to J.E.G (e-mail: Email: jgalag@mit.edu) or B.B. (e-mail: Email: bwb@genome.wi.mit.edu). The whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession AABX00000000. The version described in this paper is the first version, AABX01000000.

Abstract

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes—more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca²⁺ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.