Utilizing Cutting-Edge Computational Biology Methods in the Genomic Analysis of Florida Endangered Species

Over the past decade, the technologies used to obtain sequencing data from biological tissues have significantly improved. This has resulted in a marked increase in the ability of biological researchers to collect unprecedented quantities of large-scale DNA sequence data in a short timeframe. Recent developments in genome sequencing algorithms have allowed bioinformatics utilities to begin to take full advantage of this data, paving the way for significant increases in our understanding of genomics. New methods of genomics research have now created many new opportunities for discoveries in fields such as conservation ecology, personalized medicine, and the study of genetic disease. This research project consist of two major components: the utilization of recently-developed computational biology methods to perform sequence assembly on native Florida Species, and the creation of new bioinformatics utilities to facilitate genomics research. This project includes the completion of the first stage of the Florida Endangered Species Sequencing Project, the assembly and annotation of the transcriptome of the Florida wolf spider: Schizocosa ocreata, and a preliminary analysis of differential gene expression in ocreata organisms. Initial work is also included on Florida Endangered Species Sequencing Project Stage Two: sequence assembly projects for the Florida Manatee and the Gopher Tortoise. Discussion is included of two new computational biology utilities: TFLOW, a transcriptome assembly pipeline designed to facilitate de novo transcriptome assembly projects, and ongoing development of the GATTICA web-based bioinformatics toolkit. The TFLOW package has been released for download through the FSU Center for Genomics and Personalized Medicine.