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

转座元件(TES)是一种可移动的遗传元件，可增加其在整个基因组中的拷贝数。它们通常构成基因组的相当大比例；例如，玉米基因组由大约50%到70%的TES组成。尽管它们普遍存在，但TES的基因组效应相对未知。它们可以插入到功能基因中，干扰基因功能，并对生物体产生负面影响。然而，它们的流行也表明它们有时可能是有益的。该项目的目标是使用进化方法系统地评估在整个拟南芥基因组中插入TE的进化效果。为了做到这一点，我们将在A.thaliana基因组序列中鉴定TES，然后评估TES是否在许多不同的个体中发现。通过评估它们在个体中的流行程度，我们将能够推断进化史，从而为TES对基因组功能的影响提供重要的见解。这项拟议的工作将对科学产生两方面的影响。首先，这将是第一次对TE插入的进化影响进行全面的、全基因组的评估。在这一过程中，它将提供关于不同TE类型的进化动力学和基因组生物学的迫切需要的信息。其次，该提案是围绕本科教育而设计的。本科生将指导大部分实验部分，他们将通过PI每周一次的课程接受实验室研究、生物信息学、科学写作和科学演示方面的培训。这些学生还将为加州大学欧文分校正在进行的外展工作做出贡献。

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.