UC Merced

Spliceosomal introns, sequences interspersed throughout genes that are removed during mRNA production by machinery called the spliceosome, are a hallmark feature of eukaryotic genomes and gene structure. They are ancient genomic elements which can vary widely in number and size between species, and have remained a puzzling aspect of genome evolution in the decades since they were first discovered. To make the situation more complicated, there are in fact two separate spliceosomal systems, termed major (or U2) and minor (U12), which are responsible for the removal of ≥ 99.5% and less than half a percent of introns in most genomes, respectively. Minor introns in particular display a puzzling evolutionary pattern: in many cases, they are maintained with high degrees of conservation between deeply-diverged species, yet in others are either mostly or entirely missing. A large amount of the foundational work on minor introns was completed before the advent of next-generation sequencing, and almost all of the existing comparative genomics work in the field involves fewer than a dozen or so model organisms. In addition, the primary resources used by the field to identify minor introns are static databases containing information on a limited number of species. This dissertation contributes to our understanding of minor introns over the course of four distinct but related projects: First, it describes an effective and accessible method for identifying minor introns in intron sequence data, as well as the creation of a database containing the largest collection of minor intron orthology data available. Second, this dissertation highlights an extraordinary case of minor intron enrichment in a slime mold genome, reshaping our understanding of the limits of minor intron evolution. Third, it contains a sweeping analysis of minor intron diversity across more than 3000 eukaryotic genomes, uncovering a number of novel aspects of minor intron evolution and providing a rich substrate for future work. Finally, this dissertation describes a novel finding of a fungal genome with significant numbers of minor introns, and uses it to attempt to clarify a set of longstanding theories about the role of minor introns in eukaryotic evolution.