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Spliceosomal evolution in the reduced genomes of microsporidia Whelan, Thomas


Eukaryotic genes are mosaics of coding regions and non-coding regions called spliceosomal introns. Introns are removed from pre-mRNA by a ribonucleoprotein complex called the spliceosome. The spliceosome in humans is composed of five small nuclear RNAs and nearly 200 associated proteins. As nuclear genomes reduce, introns are more readily lost and, as a result, there is weakened selection to maintain a complex spliceosome. My dissertation focuses on the evolution of introns and spliceosomes in species with reduced genomes. Microsporidia are intracellular parasites that have extremely reduced nuclear genomes and have lost of many, if not all, introns. I examined all available microsporidian genomes and identified a family of introns that are conserved in all intron-containing microsporidia. These introns differ from typical microsporidian introns: they are longer, are spliced at higher levels, have hyperextended motifs, and contain internal conserved regions that may indicate a non-coding function. Despite the genome of Pseudoloma neurophilia having no annotated introns, I identified the presence of two long introns. I established that the P. neurophilia spliceosome is the most reduced known, and that the retained proteins and small nuclear RNAs are notably divergent from canonical orthologs. Due to extensive sequence evolution in microsporidia, direct comparisons to model organisms can be difficult. I produced the first transcriptomes from the Rozellomycota, the sister group to microsporidia, and found significant plasticity of expression throughout the lifecycle. I also found that Rozella introns are extremely constrained in size but lack conserved spliceosomal motifs. These data, combined with available genomic data from two other related parasites, provide insights into the evolution of microsporidian introns. Spliceosomal reduction extends beyond the loss of proteins. In the red alga Cyanidioschyzon merolae, a regulatory toggle in the core spliceosomal protein Prp8 has been lost. I examined a diverse set of eukaryotes and found that convergent losses occurred in other reduced taxa, including microsporidia. Overall, my dissertation highlights the usefulness of microsporidia as a model for spliceosomal reduction and aids in our understanding of the evolution of splicing in reduced systems.

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