MUII Dissertation Defense-Lynsey Whitacre

Alternative Applications of Whole Genome De Novo Assembly in Animal Genomics  

Improvements in whole genome sequencing technologies have allowed substantial increases in the amount of data that can be generated on a single individual. This has facilitated many de novo genome assembly projects in the animal sciences. The overarching goal of de novo assembly is to overlap sequencing reads to construct contiguous sequences, also known as contigs or scaffolds, representing the genome. Once a high quality de novo assembly is constructed, it is often used to determine variation in the genome or simply as a reference for future resequencing projects. However, the nature of de novo assembly algorithms lends the method to contribute information about other characteristics of an animal’s genome. The research presented in this dissertation aims to maximize the use of de novo assemblies from both RNA and DNA sequencing to answer questions about animal genomics in the absence of other established genomics or bioinformatics tools designated for that purpose. These questions include detection of commensal and parasitic organisms in cattle, runs of homozygosity pertaining to a genetic defect in water buffalo, and population-level and species-level variation in a threatened catfish.