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The consequences of transposable element and DNA methylation on plant genomes


Plant genomes are not static; they are constantly being transformed by nucleotide substitutions, the propagation of mobile DNA, and epigenetic modifications. In the three chapters of my dissertation, I show how plant genomes are shaped by transposable elements (TEs) and DNA methylation. In the first chapter, I test the hypothesis that DNA plmethylation is involved in differential gene expression between plant tissues. To explore this hypothesis, I measured whole genome DNA methylation and gene expression in leaf and floral bud tissue from Brachypodium distachyon. I found that differential CG methylation in the promoter region explains ~10% of the variation in gene expression between tissues. The second chapter examines the two modes that a plant uses to silence TEs, and I specifically question why both are necessary for efficient TE containment. I address this question by creating a mathematical model of ordinary differential equations that represents the interactions between TE propagation and epigenetic silencing, including DNA methylation. The model suggests that both modes are crucial for efficient silencing, and it also suggests that TE retention leads to more robust silencing. Finally, the third chapter predicts that, because of their deleterious nature, TEs will be ‘purged’ from a lineage that has undergone inbreeding. To test this, I examined the properties of maize genomes that were subjected to inbreeding for six generations. Over a total of 11 inbred lines, I measured genome size with cell flow cytometry and characterized genome content by whole genome sequencing. The results revealed evidence that genome size decline is associated with TE loss in a subset of inbreeding lines and provided an opportunity to consider potential mechanisms for TE removal.

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