UC Santa Cruz

Technologies used to sequence and assemble genomes have developed rapidly in the past decade, such that the money and time required to sequence a genome have both fallen by a factor of 10,000. This has given scientists new tools to study a wide variety of questions in biology. In this thesis, I first discuss some of these new technologies and the scientific advances they have facilitated. During my graduate studies, I worked on three different projects that involved producing long-range genome assemblies with these new technologies and/or using these assemblies along with transcriptomic data to answer biological questions about the regulatory architecture of genomes. The first project I discuss is the assembly of a new reference genome for the domestic horse. A reference assembly of the domestic horse genome was released in 2007 using the best genomic technologies available at the time. Along with collaborators, I used data from new technologies not available in 2007 to assemble a new genome with improved contiguity, completeness, and accuracy. This work provides a resource for horse geneticists studying regulation of gene expression, among other subjects. The next project I discuss is about temperature-dependent sex determination in the American alligator. Unlike in humans, the sex of an alligator is determined by the temperature at which its egg is incubated. I used a new long-range genome assembly, RNA sequencing, and differential expression analysis to test a hypothesis about the role of estrogen in regulating gene expression during temperature-dependent sex determination. [final chapter embargoed]