Evolutionary Dynamics of Transposable Elements in Selfing Arabidopsis Thaliana and its Outcrossing Relative

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Transposable elements (TEs) are mobile genetic elements that increase their copy number throughout a genome. They often constitute a substantial proportion of a genome; for example, the maize genome consists of ~ 50% to 70% TEs. Despite their prevalence, TEs' genomic effects are relatively unknown. They can insert into functional genes, interrupt gene function, and negatively affect an organism. However, their prevalence also suggests that they may be beneficial on occasion. The goal of this project is to use evolutionary approaches to systematically evaluate the evolutionary effect of TE insertions throughout the Arabidopsis thaliana genome. To do this, we will identify TEs in the A. thaliana genome sequence and then assess whether the TEs are found in many different individuals. By assessing their prevalence among individuals, we will be able to infer evolutionary histories, thereby providing important insights into the effect of TEs on genome function. The proposed work will impact science it two ways. First, it will be the first comprehensive, genome-wide evaluation of the evolutionary effect of TE insertion. In the process, it will contribute much needed information about the evolutionary dynamics of different TE types and genome biology. Second, the proposal has been designed around undergraduate education. Undergraduates will conduct much of the laboratory component, and they will receive training in lab research, bioinformatics, scientific writing and scientific presentation through a weekly course taught by the PI. The students will also be expected to contribute to ongoing outreach efforts at UC Irvine.