The overall goals of this project are to develop and share computational tools for comparative analysis of fungal genomes, and to apply these tools to available genome data to address key questions about genome evolution, genes, and regulatory elements. The project addresses three related problems in comparative genomics: (a) detecting synteny and genome rearrangement between organisms over a range of evolutionary distances, (b) improving gene prediction through comparative analysis, and (c) detecting and characterizing conserved non-coding elements. The specific objectives are to (1) develop a hierarchical clustering-based algorithm for characterizing synteny between related organisms, (2) utilize comparative sequence analysis to improve fungal gene annotations, (3) utilize comparative sequence analysis to identify and characterize conserved non-coding elements, (4) experimentally validate conserved upstream open reading frames (uORFs), and (5) apply these methods to analyze available genome sequences from clusters of related fungi and make the results publicly available.
This work will contribute to the understanding of fungi and to the ability to exploit these organisms for the benefit of mankind. It will also contribute to the scientific understanding of all eukaryotic genomes, including that of humans, through the development of tools for interpreting genome sequences. It will foster biological insights into the myriad of cellular processes that fungi, plants, and animals share. In addition, the project will contribute to the training of computational biologists by involving students ranging from undergraduates to postdoctoral fellows. Students in the Minority Outreach Program at the Broad Institute will also be recruited for the project.
