? The short life cycle and small genome size of X. tropicalis (1,700 Mb, or half the genome size of X. laevis) make tropicalis a better vertebrate model system than X. laevis to study developmental genetics. This project plans to sequence and annotate more than 50 developmental genes, gene families and surrounding regions on X. tropicalis BAC clones in one year. The average size of each region will be about 70 Kb, which will include the coding sequences along with the adjacent up-stream and down-stream sequences that may harbor the regulatory elements. The total sequence involved will be about 4 million base pairs. Specifically, this project will: ? ? (i) Obtain BAC clones containing development-related genes from a X. tropicalis BAC library. ? (ii) Localize each gene of interest on BACs and select the BAC with the gene of interest in the center of the insert. ? (iii) Sequence selected BAC clones to contiguity within and around the genes of interest. ? (iv) Analyze and annotate BAC sequences for genes, potential cis-regulatory elements, CpG islands, interspersed repeats, and other features deemed of interest as the project unfolds. ? (v) Whenever X. laevis sequence or relevant sequences from other species is available, perform cross-species analyses to identify conserved sequence blocks that might serve as candidates for cis-regulatory elements and modules. ? ? This project will rapidly provide a set of finished and annotated sequences for development- related genes in the X. tropicalis genome and badly needed information for investigating the mechanisms by which the developmental processes are regulated. By cross-species comparison, it will also facilitate the search for developmental genes and regulatory mechanisms among different species including human and help to study development related human diseases. The long-term goal of this project is to combine genomic sequence knowledge with sophisticated embryological and proteomics methods to study developmental genetics in this important vertebrate system and other biological systems. ? ?
