Thesis

An Investigation of Retroelements in Clintonia Uniflora

The C-value paradox, which is the lack of correlation between genome size and organism complexity, was the focus in many early studies of the genome. The "paradox" has now been resolved and can be explained by the presence of transposable elements. Transposable elements can constitute up to 90% of an organism's genome. It is these transposable elements, specifically retroelements, which account for the differences seen in genome sizes of higher plants. In this thesis, three major classes of retroelements (Ty1/Copia-, Ty3/Gypsy- and LINE-like elements) were studied in Clintonia uniflora, a member of the Family Liliaceae. Retroelement phylogeny, composition, abundance and activity were investigated in this species and, in addition, the relative abundance of retroelements in four other members of the Order Liliales was examined as part of a larger study on genome expansion in the Liliales. Degenerate primers, which allow for amplification of diverged retroelement sequences for the reverse transcriptase region, were used to amplify the retroelements. Subsequent cloning and sequencing of the elements indicate that retroelements have indeed been a contributing factor in the evolution of the Clintonia uniflora genome, with the most recent amplification being a group of Ty1/Copia-like elements. In addition, this work showed the presence of an older, diverse population of copia and gypsy elements in the Clintonia genome. In studying retroelement copy number in Clintonia, it was determined that there is a higher copy number of copia elements than gypsy elements in the genome, with minimal contribution from LINEs. Analysis of retroelement activity in Clintonia, in frozen and living leaf tissue and callus tissue, was inconclusive. An examination of retroelement abundance in other members of the Order Liliales showed variable copy numbers of copia- and gypsy-like elements in the genome. In all the species examined, however, there were significantly more Ty1/Copia-like elements than Ty3/Gypsy-like elements. In addition, retroelement abundance in the species was roughly proportional to genome size, with a few intriguing discrepancies. This study reveals the contribution of retroelements in the evolution of the Clintonia uniflora genome, as well as their relative abundance in the genomes of related species and lays the foundation for future studies in mechanisms of genome expansion in the Liliales.

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