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

拟南芥自交及其异交近缘转座因子的进化动态

• 批准号: 0316157
• 负责人: Brandon Gaut
• 金额: $ 53万
• 依托单位: University of California-Irvine
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-08-15 至 2007-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0316157&HistoricalAwards=false
• 关键词: Evolutionary; Dynamics; Transposable; Elements; Selfing

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.

转座元件 (TE) 是可移动的遗传元件，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很大一部分；例如，玉米基因组由约 50% 至 70% 的 TE 组成。尽管 TE 很普遍，但其基因组效应却相对未知。 它们可以插入功能基因、中断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来系统地评估拟南芥基因组中 TE 插入的进化效应。 为此，我们将鉴定拟南芥基因组序列中的 TE，然后评估这些 TE 是否在许多不同个体中发现。 通过评估它们在个体中的流行率，我们将能够推断进化历史，从而为 TE 对基因组功能的影响提供重要的见解。拟议的工作将从两个方面影响科学。 首先，这将是首次对 TE 插入的进化效应进行全面的全基因组评估。 在此过程中，它将提供有关不同 TE 类型的进化动力学和基因组生物学的急需信息。 其次，该提案是围绕本科教育而设计的。本科生将进行大部分实验室部分，他们将通过 PI 每周教授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。 学生们还将为加州大学欧文分校正在进行的外展工作做出贡献。