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Studies on the dinoflagellate genome McEwan, Michelle Louise


Dinoflagellates are unusual eukaryotes in many ways, but one of the most interesting features of this cell - its enormous genome - is not well studied because its sheer size is an obstacle to sequencing. Genome expansion can be the result of polyploidy, intron gain, mobile genetic elements, or large intergenic regions. I have studied organellar genome reduction in Kryptoperidinium foliaceum, intron composition in Heterocapsa triquetra and Karlodinium micrum, and surveyed genomic DNA from H. triquetra in order to get a better grasp on mechanisms of genome expansion in dinoflagellates. K. foliaceum has replaced its ancestral red algal plastid with a diatom plastid via tertiary endosymbiosis. Gene transfer from endosymbiont to host nucleus has likely occurred, but this endosymbiont is much less reduced than well-studied secondary endosymbiotic intermediates, the cryptophytes and chlorarachniophytes, where relict nuclear genomes (nucleomorphs) are retained. I sequenced the first protein-coding genes from the K. foliaceum endosymbiont and host nuclear genomes. I have characterised genes for nucleus-encoded cytosolic proteins, actin, alpha-tubulin, beta-tubulin, and HSP90, from both host and symbiont nuclei of K . foliaceum. Phylogenies show that the actin is diatom-derived, the beta-tubulin dinoflagellate-derived, while both diatom- and dinoflagellate-derived alpha-tubulin and HSP90 genes were found. The presence of these genes implies they are still functional and that the endosymbiont is at an earlier stage of genetic reduction than those of cryptophytes or chlorarachniophytes, Thirteen of 16 known dinoflagellate introns are non-canonical. I amplified and screened 63 K. micrum and H. triquetra genes, but found no introns. I report that introns are neither abundant in dinoflagellate genomes, nor have they played a major role in dinoflagellate genome expansion. I built a genomic DNA library for the dinoflagellate, H. triquetra, and sequenced 214 fragments (23 l,164bp). Main features of this library include imperfect complex repeats, retrotransposon domains, 53% G C content, few open reading frames (ORFs), and a lack of identifiable protein-coding regions. These results support mobile elements and repeats as major sources of DNA in expanded dinoflagellate genomes. The best explanation for the huge amounts of rion-coding DNA remains the idea that it functions as a structural scaffold and contributes to chromosomal organization.

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