DISSERTATION RESEARCH: Evolutionary impact of genome duplication on alternative splicing: Genome-wide assessment in a polyploid plant (Tragopogon)

本研究将探讨全基因组复制对遗传多样性的影响。当一个完整的基因组加倍时，所产生的生物体被称为多倍体。这些事件具有巨大的经济和生物学意义。大多数农作物都是多倍体，这种复制创造了世界上大部分的植物和动物多样性。复制后，基因数量、表达和调控经常发生进一步的变化。这样的修饰能产生我们所看到的所有遗传和生态多样性吗？我们知道当基因被翻译成蛋白质时，基因片段可以在一个被称为选择性剪接的过程中重新排列。 基因组复制后的剪接是否会进一步增加多样性？通过研究复制后剪接模式的变化，这项研究将有助于确定是什么产生了遗传多样性。这些信息有助于我们了解生物多样性。它对多倍体作物也有重要的经济意义。将向K-12学生开展外联活动，并将为高中生开发一个新的农业课程单元。本研究的目的是探讨RNA选择性剪接（AS）在开花植物角龙（Tragopogon，goatsbeard;向日葵科）中最近形成的自然多倍体物种中的作用和程度。该属植物包括两个物种，起源于多倍体仅80年前。它们可作为研究近期和复发性基因组复制（GD）的天然模型。本研究将多倍体T.与二倍体亲本杂交（T.和T. pratensis)。本文将回答以下几个有关多倍体物种AS的核心问题：（1）T.偏离其双亲的平均值还是与双亲高度偏离？ (2)在独立来源的自然人群中，GD后AS是否会重复发生相同的变化？(3)相反地，AS的各个方面是否高度可变，并且在多倍体的一个形成与另一个形成之间存在差异？为了解决这些问题，我们克隆了二倍体T.并将其作为全基因组AS检测的参考。该基因组还将具有潜在的经济价值，因为角龙与重要作物莴苣密切相关。功能注释，包括基因本体富集分析，将用于检查哪些生物学功能（例如光合作用）与GD后AS模式发生变化的基因密切相关。

This research will investigate the impact of whole genome duplication on genetic diversity. When an entire genome is doubled the resulting organism is said to be polyploid. Such events are of enormous economic and biological importance. Most agricultural crops are polyploid, and this duplication created much of the world's plant and animal diversity. After duplication, further changes often occur in gene number, expression, and regulation. Can such modifications generate all the genetic and ecological diversity we see? We know that when genes are translated into protein, genetic pieces can be rearranged in a process called alternative splicing. Does splicing following genome duplication further increase diversity? By studying changes in splicing patterns following duplication, this research will help determine what produces genetic diversity. This information help us understand biodiversity. It also has important economic implications for polyploid crops. Outreach to K-12 students will occur, and a new class module on agriculture for high school students will be developed. The goal of the proposed research is to address fundamental questions regarding the role and extent of RNA alternative splicing (AS) in a recently formed naturally occurring polyploid species in the flowering plant Tragopogon (goatsbeard; sunflower family). This plant genus includes two species that originated via polyploidy only 80 years ago. They serve as natural models for the study of recent and recurring Genomic Duplication (GD). This research will compare the polyploid T. miscellus to its diploid parents (T. dubius and T. pratensis). The following central questions about AS in polyploid species will be answered: (1) Are the patterns of AS in T. miscellus the average of its parents or highly divergent from the parents? (2) Do the same changes in AS occur repeatedly following GD in natural populations of independent origin? (3) Conversely, are aspects of AS highly variable and differ from one formation of this polyploid to the next? To address these questions, a nuclear genome sequence of the diploid T. dubius will be constructed and used as the reference for genome-wide AS detection. This genome will also be of potential economic value because Tragopogon is closely related to lettuce, an important crop. Functional annotation, including gene ontology enrichment analysis, will be used to examine which biological functions (e.g. photosynthesis) are closely linked to genes with changes in AS patterns after GD.