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Abstract
The evolution of new phenotypes can arise by changes to DNA encoding amino acid sequences, impacting protein function, or by changes to non-coding regulatory DNA, impacting gene expression patterns. Comparative analyses between lineages across phylogenies is a powerful approach for inferring the genotypic basis of phenotypic innovations. The advent of modern nucleotide sequencing technologies has enabled the resolution of evolutionary relationships spanning up to entire kingdoms, which has provided a framework for comparisons stretching back hundreds of millions of years. Studies of gene expression have also benefitted immensely from advances in sequencing technologies, since it is now possible to obtain snap shots of the entire transcriptome of nearly any species, cell type, developmental stage, or experimental treatment condition. Given these advancements, it is expected that integrative phylogenomic studies of gene expression will continue to proliferate. Here, I use comparative phylogenomics to characterize the evolution of gene expression patterns that have given rise to Crassulacean acid metabolism in two Yucca species that contrast in photosynthetic modes. This study revealed that evolution of both time-structured expression patterns and changes to overall expression magnitude of orthologous genes contributed to the evolution of CAM in Y. aloifolia. I demonstrate that in many cases, time-structured expression patterns were present before the divergence of Y. aloifolia and Y. filamentosa. I also assess species-wide patterns of expression pattern evolution, which revealed an extensive amount of evolution over approximately 12 million years since the divergence of C3 and CAM Yuccas. In the second half of this work, I scanned six Angiosperm species for evidence of polycistronic gene expression, which is thought to be exceedingly rare in Eukaryotes, however limited examples have been described in fungi¬, plants and animals. Evidence for widespread conserved or independently evolved polycistronic expression would add to knowledge of modes of eukaryotic expression that may be leveraged for genetic engineering purposes. While the survey did not reveal strong evidence for polycistronic expression, the analysis methodology proved useful for identifying errors in the surveyed reference genome annotations and provides a simple and effective framework for easily assessing any species for polycistronic expression.