Tetrahymena thermophila is a very useful genetic, unicellular, animal model for fundamental eukaryotic experimental cell and molecular biology and for comparative genomics. It shares a high degree of functional conservation with human and animal biology. Its genome sequence, whole-genome assemblies and gene predictions are publicly available at the TIGR website. Powerful molecular genetic technology is available for sequence-enabled experimental work. Forward genetics is a general and powerful way to approach the investigation of biological phenomena and Tetrahymena, for all of the above reasons, is an excellent organism for forward genetics. A complete genetic map of its genome linked to completely assembled genome sequence is essential for this purpose. The goal of this project is to generate such complete, fully integrated genetic maps and sequence assemblies. To accomplish the goals of this project, we aim to: 1) Complete the physical map of the somatic (macronuclear or MAC) genome by identifying the links between open-ended sequence scaffolds in order to construct complete higher order assemblies, each representing one of the approximately 275 MAC chromosomes. 2).Complete the assembly of the germline (micronuclear or MIC) genome by ordering and orienting the predicted approximately 275 MAC chromosome assemblies along the MIC chromosomes. "HAPPY" physical mapping will be used to accomplish both aims 1 and 2. 3) Exploit short tandem repeats to identify and genetically map at least one DNA polymorphism in every MAC chromosome assembly, and relate each of these polymorphisms to the MIC and MAC genetic maps. It will then be possible to assign any mutant gene with a biologically significant phenotype to its fully assembled and gene- annotated MAC chromosome sequence scaffold, without relying on any feature other than its phenotype. Achievement of these aims will greatly enhance the value of the high quality Tetrahymena whole genome sequence for fundamental, biomedical and biotechnological research. This project will also generate methodology, data, and resources generally useful to the scientific research community for the investigation of important biological mechanisms. Given the genome-wide outlook of our proposal and Tetrahymena's experimental user-friendliness, this work ought to provide opportunities to discover unanticipated phenomena of biological interest. [unreadable] [unreadable] [unreadable]