the Neurospora Genome Project
at the University of New Mexico
The Neurospora Genome Project (NGP) represents an effort to obtain partial or complete nucleotide sequences from a large number of cDNA clones derived from conidial, mycelial, unfertilized sexual and perithecial libraries of N. crassa. A collaboration with the University of Georgia is underway to develop a detailed physical map of the N. crassagenome.
A major goal of this research is to identify putative Neurosporahomologs of known genes in other organisms. You can view this list here. You can also search the NGP database or other Neurospora databases here. Before using the search page, please read the IMPORTANT note concerning the sequence format on this web page.
Services Available from the NGP
These databases include the NeurosporaEST database we have generated during the Neurosporagenome project as well as Neurospora nucleotide and Neurosporaprotein databases, which contain published sequences from Neurosporaspecies.
Search any of these Neurosporadatabases that we have available using either the BLAST (Altschul et al. 1990) or FASTA (Pearson & Lipman 1988) algorithms.
To use the search page, enter your sequence in FASTA format. This format involves placing ">sequence name" before the text of your sequence. The sequence name is optional but the ">" is not.
We are in the process of improving our search page, and there will be greater tolerance for different sequence formats in the near future. If you have problems using this page, please email the Neurospora Genome Project at email@example.com.
We have categorized all of the NeurosporaESTs that show significant identity to proteins that have been sequenced in other organisms according to a slightly modified version of the EGAD scheme (White & Kerlavage 1996). If you use this information please cite Nelson et al. (1997).
Restriction fragment length polymorphisms (RFLPs) can be used to determine the approximate map location of any cloned piece of DNA. To establish an RFLP mapping system for N. crassa, R.L. Metzenberg and coworkers crossed strains with multiple sequence differences, Oak Ridge laboratory strains (designated "O") and a Mauriceville-1c wild-collected strain (designated "M"; Metzenberg et al. 1984 Neurospora Newsl. 31:35-39; ibid. 1985 Proc. Natl. Acad. Sci. U.S.A. 82:2067-2071; Metzenberg and Grotelueschen 1995 Fungal Genet. Newsl. 42:82-90). Progeny from two separate crosses have been widely distributed and used for mapping. For the first cross, 38 progeny from ordered asci were analyzed; since nonsister spores from the same half of the ascus were selected, first-division segregation can be distinguished from second-division. For the second cross only 18 random ascospore progeny were analyzed, and the small numbers limit resolution capabilities. Given this limitation, we encourage researchers to use the first cross for RFLP mapping. We have developed a Neurospora RFLP mapping program for the first cross to facilitate placement of new loci. See Nelson et al. (1998) for program details.
Efforts are underway to sequence the entire genome of Neurospora crassa. A German consortion coordinated by Dr. Ulrich Schulte (at the Institute of Biochemistry,
Heinrich-Heine-University, D-40225 Duesseldorf) is sequencing two chromosomes (linkage groups II and V); this project is supported by the Deutsche Forschungsgesellschaft (DFG). BLASTN and BLASTP similarity searches can be run against the linkage group II and V sequences.
The Neurospora Policy Committee (Mike Plamann (Chair), Mary Anne Nelson, Dan
Ebbole and Eric Selker) has established a Neurospora Genomics Policy Committee (NGPC) to coordinate and report on efforts to advance genome undertakings. The purpose of the NGPC is to
promote Neurospora genome research. The primary role of the NGPC is to facilitate communication between the Neurospora community and established sequencing groups that might efficiently complete the genome sequencing. The NGPC is charged with providing a venue for members of the community to organize genome projects and will serve as a clearing house for all Neurospora genome efforts. The initial members of the NGPC are: Mary Anne Nelson (chair), Kathy Borkovich, Jay Dunlap, Matthew Sachs, Ulrich Schulte and Eric Selker.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403-410.
Nelson, M. A., Crawford, M. E. and Natvig, D.O. (1998). Restriction polymorphism maps of Neurospora crassa: 1998 update. Fungal Genetics Newsletter 45, 44-54.
Nelson, M. A., Kang, S., Braun, E. L., Crawford, M. E., Dolan, P. L., Leonard, P. M., Mitchell, J., Armijo, A. M., Bean, L., Blueyes, E., Cushing, T., Errett, A., Fleharty, M., Gorman, M., Judson, K., Miller, R., Ortega, J., Pavlova, I., Perea, J., Todisco, S., Trujillo, R., Valentine, J., Wells, A., Werner-Washburne, M., Yazzie, S., and Natvig, D. O. (1997). Expressed sequences from conidial, mycelial and sexual stages of Neurospora crassa. Fungal Genetics and Biology 21, 348-363.
Pearson, W. R., and Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences USA 85, 2444-2448.
White, O., and Kerlavage, R. (1996). TDB: New databases for biological discovery. Methods in Enzymology 266, 24-40.
Generous support from the National Science Foundation is gratefully acknowledged.