Neurospora crassa has been an important research organism for the past half century, and the field of biochemical genetics was initiated using Neurospora. Over one thousand genes have been identified by mutation and mapped, making N. crassa the best-studied filamentous fungus. Now, with the identification and characterization of large numbers of expressed genes, the goal of connecting the genes of Neurospora to their biochemical functions is becoming reality. The Neurospora Genome Project (NGP) at UNM involves the new science of functional genomics (analysis of the complete set of genes of an organism). The long-term goal of the NGP is the characterization of the majority of the genes of Neurospora and the association of those genes with biological function. In previous analyses, the NGP showed that the majority of the genes being studied are novel (not yet identified in any other organism). It is predicted that the project will provide novel information in the areas of genetics, metabolism, biochemistry, and evolution. Based on the history of development of new technologies, the research will likely lead to industrial applications, as well as advances in pharmaceutical, environmental and basic research. The genetic complement of N. crassa will be investigated using an expressed sequence tag (EST) approach, whereby partial complementary DNA (cDNA) sequences are obtained and used to identify distinct genes and in many cases predict their function (when a homologous gene has been characterized). The genetic complement of N. crassa will be investigated in the context of how its expression relates to the developmental decisions made by the organism. ESTs from four cDNA libraries, corresponding to the genes expressed in germinating conidial, advanced-growth mycelial, unfertilized sexual and perithecial (sexual) tissues will be analyzed. Also, a concerted in silico analysis will be directed to the characterization of those cDNAs apparently lacking homologs in other organisms. Transcriptional profiling, or cDNA microarray analysis, will be used to determine the relative levels of expression of thousands of genes simultaneously, and the role these changes play in development will be examined. The microarray analysis will focus on changing patterns of gene expression as the organism switches from vegetative growth to formation of the female sexual structure, and then progresses through sexual development to form the sexual progeny. The genes controlled by the products of the mating type loci and the white collar genes, all thought to be transcriptional regulators, will also be determined. The Neurospora Genome Project includes an important educational component. As an integrated part of the research, undergraduates and graduate students are trained in molecular genetics and computational biology (functional genomics). The students benefit greatly by working together toward a common goal, and the program had the additional advantage of exposing each student to diverse concepts and techniques. The students are involved in problem-solving and decision-making at all levels. In collaboration with the Albuquerque High Performance Computing Center (AHPCC) at UNM, the NGP will continue to provide open access to a server for web-based BLAST and FASTA searches of the NGP EST database and specialized databases containing all published Neurospora nucleotide and protein sequences. In addition, all of the Neurospora ESTs with significant identity to genes that have been sequenced in other organisms will be classified by function; updates of this proteome analysis can be accessed from the NGP web page [http://biology.unm.edu/~ngp/home.html]. The abundance of genes already identified by mutation and mapped in N. crassa will facilitate the association of sequenced cDNAs with genes of known function. The correlation of the genetic and physical maps will become ever more refined, simplifying the association. The enormous amount of effort devoted to the genetic characterization of Neurospora over the last sixty years will yield enormous dividends, in the form of identified genes, rational and rapid development of testable hypotheses, and stimulation of many areas of fungal research.