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Long-range assembly and transcriptomics elucidate the regulatory architecture of three vertebrate genomes

Abstract

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]

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