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An improved SNP map for Neurospora crassa Mauriceville

Kyle R. Pomraning, Kristina M. Smith and Michael Freitag,

Dept. of Biochemistry and Biophysics, Program for Molecular and Cellular Biology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis OR 97331 (contact: freitagm@onid.orst.edu)

We have sequenced the genome of FGSC2225 from Mauriceville, Texas (MV), the most commonly used non Oak Ridge (OR) wild type N. crassa strain for RFLP or SNP mapping (Metzenberg, RL et al. 1984. N. Newsletter 31:35-39). While we are currently preparing a complete analysis of this genome for publication, we wish to give Neurospora researchers access to a subset of the data, with the hope of accelerating current mapping projects. Over 40 sites described in the accompanying files downloadable from the FGSC website (http://www.fgsc.net/) were validated by RFLP, and another 29,612 sites were compared in silico to existing EST data from the MV strain (see http://www.broadinstitute.org/annotation/genome/neurospora/Home.html). More than 94% of all SNPs were found to be correct, as we applied a high stringency cut-off for this list. This does not,however, ensure that every individual SNP is correctly predicted (if users find inconsistencies please contact the authors). Text files are presented in “gff3” format, which allows mapping to the OR mat A reference genome available at the Broad Institute (assembly 10) and visualization by genome browsers. Only SNPs that map to a commonly used restriction endonuclease site are listed here. Sites are present and cleavable in OR but absent in MV.

The columns in the accompanying files are defined as follows:

Column 1: supercontig_nt from beginning of supercontig_OR nt change to MV nt_site that will cleave OR but not MV DNA

Column 2: not used

Column 3: Type of feature (SNP)

Column 4: Start of feature

Column 5: End of feature

Column 6: not used

Column 7: Strand (all top strand)

Column 8: not used

Column 9: ID (for mapping to Argo)

1 2 3 4 5 6 7 8 9

1_5763_T->C_TaqI . SNP 5763 5763 . + . ID=1_5763_T->C_TaqI