NSF Award
0078148
A genome contains all the instructions needed to define the biological aspects of an organism. The ability to read the DNA sequence of genes initiated a revolution in molecular biology. Recent technological advances have made it possible to determine rapidly the sequence not only of individual genes but also of entire genomes. This is critical for understanding cellular processes because the expression and function of each individual gene reflects complex regulatory pathways encoded by multiple interacting genes. The availability of genomic sequence is the single most important resource for understanding the biology of an organism. The genome of the fungus Neurospora crassa will be sequenced through a partnership between the Whitehead Institute/MIT Center for Genome Research (WI-CGR) and members of the Neurospora research community. The objectives of this study are to determine within one year the complete sequence of the 43 Mb Neurospora genome, and to make a highly accurate version of this sequence publicly available. This work will produce annotated sequence and large insert clones with endpoints precisely known with respect to the sequence that can be used for ongoing functional studies. While the result will be a clear boost in research productivity, sequencing the Neurospora genome is not, in itself, a research activity. It is a production activity in which proven methods will be applied at a specified rate to achieve a predetermined and easily measured product. The methods for producing the sequence, including shotgun sequencing, detection, and assembly, and the requisite database tools for handling the sequence are already employed at WI-CGR at a scale considerably greater than is necessary for the Neurospora project. WI-CGR has a long history of managing successful large scale projects for genome mapping and sequencing and is engaged in several genome sequencing projects, including human and mouse. The WI-CGR employs factory-style laboratory automation, automated software for data collection and analysis and a production environment that stresses high quality and reliable delivery at extremely high-throughput. The WI-CGR has worked aggressively to become the most efficient publicly funded high-throughput sequencing center in the world, as well as the leader in sequence output. The low cost of this project reflects the economies of scale, in which highly efficient utilization of personnel, equipment and reagents provides great cost savings on a per read basis. The low repeat content of Neurospora makes it ideally suited to whole genome shotgun sequencing, in which paired reads from the ends of random plasmid clones are assembled. In the first phase of the project approximately 1.2 million sequencing reads will be generated and assembled to provide on average 9X depth of coverage of the genome. Subsequent work involves both automatically-selected and human-directed sequence reads needed to close gaps and attain uniformly high sequence quality. Sequence assemblies corresponding to 3X, 6X, and 9X depth of coverage will be publicly released during shotgun sequencing and annotation and verification of the sequence assembly will commence with the 9X assembly. The biological value of this sequence is extraordinarily high because of the widespread use of Neurospora as an experimental system, the applicability of this organism to problems not addressable with other model organisms, the well developed genetic methods that will permit researchers to exploit the sequence for further experimentation, and the immediate boost it will provide to research on a large number of related organisms of economic and biological importance.
