UC San Diego

In the last decade, advances in high throughput sequencing and computational analysis of DNA and RNA have revolutionized biological research from environmental science to biomedicine. Genome and transcriptome sequences from diverse eukaryotes are now relatively easy to obtain providing unprecedented opportunities for comparative and functional genomics studies. Despite the availability of several genomes of ecologically relevant microbial eukaryotes, including the marine diatom Thalassiosira pseudonana, the application of sequence data to obtain a more complete understanding of the physiology, ecology, and evolution of eukaryotic marine microorganisms remains in its infancy. Practically, the relationship between sequence data and carbon and energy metabolism is of interest for biotechnological applications such as the engineering of algae for the development of renewable biofuels. The primary objective of this dissertation was to characterize aspects of the regulation of carbon and energy metabolism in T. pseudonana using both comparative and functional genomics approaches. In the first chapter, an analysis of the conservation of carbon partitioning enzymes was conducted by comparing three genomes of distantly related diatoms. In the second chapter, the effect of silicon starvation on the physiology and transcriptome of T. pseudonana was characterized to provide insight into the mechanisms by which metabolism is regulated at the transcript level. In the third chapter, the existence of a specific mode of transcriptional regulation (organization of genes into inverted gene pairs) was documented. Taken together, these chapters represent a significant advance in our understanding of mechanisms that regulate metabolism and cellular energetics in T. pseudonana with implications for both environmental studies and biotechnological applications.