UC Davis

Metazoa is a highly diverse clade that contains the vast majority of extant multicellular species. Complex mechanisms of transcriptional regulation are hypothesized to have greatly contributed to the increased complexity found in metazoans compared to their close unicellular relatives. These regulatory mechanisms have been well characterized in a limited number of bi- laterian animals, but have gone largely uncharacterized in non-bilaterian clades. Non-bilaterian metazoan clades emerged hundreds of millions of years ago, and can therefore provide insight into metazoan evolutionary history beyond what can be discerned from studying bilaterians alone. Thus, there is a need for resources to study transcriptional regulation in these understudied non-bilaterian clades.In this dissertation, I present an extensive set of resources characterizing transcriptional regulation in the freshwater cnidarian polyp, Hydra vulgaris. In chapter 1, I provide a general overview of the scientific literature on transcriptional regulation in non-bilaterian metazoans, with a particular focus on research conducted in Hydra. Chapter 2 contains a previously pub- lished manuscript that describes the generation of a whole-animal single-cell RNA-seq atlas for Hydra vulgaris. Chapter 3 contains a previously published manuscript that characterizes the transcriptional regulation of patterning during Hydra whole-body regeneration. Chapter 4 con- tains an unpublished manuscript that describes the generation and annotation of a chromosome- level genome assembly for the AEP strain of H. vulgaris and a high-quality draft genome assem- bly for the Innsbruck female12 strain of H. oligactis. Chapter 5 includes a summary of the work presented in chapters 1-4—including my specific contributions to chapters 2-4—and a discussion of general conclusions and future directions based on the findings presented in this dissertation.