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Wong, Donald K.

University of British Columbia

Eukaryotic genes are interrupted by non-coding regions known as introns, which are removed through pre-mRNA splicing. This process catalyzed by the spliceosome, a large complex of five small nuclear ribonucleoproteins (snRNPs), and various other proteinaceous accessory complexes. Although this process is highly conserved across eukaryotes, significant divergence is seen in organisms with reduced genomes. My dissertation research explores the evolution of nuclear pre-mRNA splicing and the spliceosome in diverse reduced algal genomes. I examined transcriptomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans for splicing in their nucleomorphs, the remnant nuclei found in their plastids. There, I observed high levels of unspliced transcripts in the intron-sparse G. theta nucleomorphs, and typical eukaryotic levels of splicing in the many tiny nucleomorph introns of B. natans. To determine if this reflects contrasting intron richness and/or differing ancestries of these plastids, I investigated splicing in three species of red algae: the mesophilic Porphyridium purpureum, and the extremophilic Cyanidiales red algae Cyanidioschyzon merolae and Galdieria sulphuraria. A comparison of transcriptome data revealed extremely low levels of splicing in the intron-poor C. merolae, typical splicing in the intron-rich G. sulphuraria, and an intermediate level of splicing in P. purpureum, whose intron richness lies between C. merolae and G. sulphuraria. My analyses present a trend where transcripts more often remain unspliced in genomes with low intron numbers, and spliceosomes exhibit increasing divergence and loss of components. I also showed that an intron’s splicing level is tied to 5′ splice site and branch donor sequence variability, suggesting an increased reliance on base-pairing for intron recognition in an increasingly reduced spliceosome. I explored potential functions of persisting nucleomorph introns of the cryptophytes Guillardia theta and Chroomonas mesostigmatica. I performed differential analysis of light and dark transcriptomes for both, and assembled a nuclear transcriptome for C. mesostigmatica, showing extensive intron retention in cryptophyte nucleomorph transcripts. However, differential splicing and gene expression is limited in nucleomorphs, suggesting that secondary plastids are primarily regulated by nuclear genes. My research highlights patterns of divergence in splicing in genomes evolving under the pressures of reduction.

Text

2022-02-11

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/80826

Botany

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/