This dissertation focuses on the transcriptome of the moon jellyfish (Aurelia sp.1). As the chapters progress, larger sets of genes are analyzed, and the work becomes decreasingly comparative in nature.
In the first chapter, I analyze the POU-class genes. I begin by using comparative genomics and "gene fishing" to resolve the topology of the POU gene tree. I then use ancestral state reconstruction to map the most likely changes in amino acid evolution for the conserved protein domains. Four of the six POU families evolved before the last common ancestor of living animals--doubling previous estimates--and was followed by extensive clade-specific gene loss. POU families best understood for their generic roles in cell-type regulation and stem cell pluripotency (POU2, POU5) show the largest number of nonsynonymous mutations, suggestive of functional evolution, while those better known for specifying subsets of neural and hormone producing cell types (POU1, POU3) appear more similar to the ancestral protein.
In the second chapter, I annotate the homeodomain repertoire for Aurelia sp.1, and compare it to data from relatives that lack a medusa life stage (Nematostella, Acropora, and Hydra). Despite having simpler life cycles, the anthozoans Nematostella and Acropora have far more homeodomains than Aurelia, primarily because of clade-specific gene expansions. The one exception to this trend is the non-anterior Hox genes, where Aurelia has seven paralogs compared to Nematostella and Acropora's two. RNA-Seq analyses suggest that these non-anterior Hox genes are expressed dynamically through the Aurelia life cycle, and therefore represent candidate genes for future studies in medusozoan bodyplan evolution.
In the final chapter, I offer a broad analysis of the developmental transcriptome for Aurelia sp.1. Two major shifts in gene expression occur during the life cycle, correlating with formation of the two "adult" morphs (the transition from primary polyp to polyp, and from polyp to strobila). The morphologically complex medusa stage that distinguishes Aurelia from other model cnidarians is not enriched in novel genes, but is enriched in many conserved cell-signaling pathways, transcription factor domains, and neuroactive receptors.