Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

• Published in: Advances in Genetics Vol. 57; pp. 49 - 96
• Main Authors: Dunlap, Jay C., Borkovich, Katherine A., Henn, Matthew R., Turner, Gloria E., Sachs, Matthew S., Glass, N. Louise, McCluskey, Kevin, Plamann, Michael, Galagan, James E., Birren, Bruce W., Weiss, Richard L., Townsend, Jeffrey P., Loros, Jennifer J., Nelson, Mary Anne, Lambreghts, Randy, Colot, Hildur V., Park, Gyungsoon, Collopy, Patrick, Ringelberg, Carol, Crew, Christopher, Litvinkova, Liubov, DeCaprio, Dave, Hood, Heather M., Curilla, Susan, Shi, Mi, Crawford, Matthew, Koerhsen, Michael, Montgomery, Phil, Larson, Lisa, Pearson, Matthew, Kasuga, Takao, Tian, Chaoguang, Baştürkmen, Meray, Altamirano, Lorena, Xu, Junhuan
• Format: Book Chapter Journal Article
• Language: English
• Published: United States Elsevier Science & Technology 2007
• Subjects: Base Sequence; Chromosome Mapping; DNA, Fungal - genetics; Gene Deletion; Gene Expression Profiling; Gene Library; Genetic Techniques; Genetics (non-medical); Genome, Fungal; Genomics; Molecular biology; Mutation; Mycology, fungi (non-medical); Neurospora - genetics; Neurospora crassa; Oligonucleotide Array Sequence Analysis; Phenotype; Polymorphism, Single Nucleotide
• ISBN: 9780120176571; 0120176572
• ISSN: 0065-2660
• DOI: 10.1016/S0065-2660(06)57002-6

A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building from the completely sequenced 43‐Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes. Oligonucleotide‐based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.