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

论文研究：基因组复制对选择性剪接的进化影响：多倍体植物（Tragopogon）的全基因组评估

• 批准号: 1701751
• 负责人: Douglas Soltis
• 金额: $ 1.98万
• 依托单位: University of Florida
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-01 至 2019-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1701751&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; Evolutionary; impact; genome

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.

这项研究将研究整个基因组重复对遗传多样性的影响。当整个基因组增加一倍时，所得生物被称为多倍体。这些事件具有巨大的经济和生物学重要性。大多数农作物都是多倍的，这种重复创造了世界上许多动植物的多样性。复制后，基因数，表达和调节通常发生进一步的变化。这样的修改能否产生我们看到的所有遗传和生态多样性？我们知道，当基因转化为蛋白质时，遗传碎片可以在称为替代剪接的过程中重新排列。 基因组重复后的剪接是否会进一步增加多样性？通过研究复制后的剪接模式的变化，这项研究将有助于确定什么产生遗传多样性。这些信息有助于我们了解生物多样性。它对多倍体作物也具有重要的经济影响。将发生与K-12学生的宣传，并将开发一个针对高中生农业的新班级模块。拟议的研究的目的是解决有关在开花植物tragopogon（Goatsbeard;向日葵家族）中最近形成的自然发生的多倍体物种中RNA替代剪接（AS）的作用和程度的基本问题。该植物属包括仅80年前通过多倍体起源的两个物种。它们是研究最近和经常性基因组重复（GD）的自然模型。这项研究将将多倍体T. miscellus与其二倍体父母（T. Dubius和T. Pratensis）进行比较。将回答以下有关AS中的中心问题：（1）AS在T. miscellus中的模式是其父母的平均值还是与父母高度分歧？ （2）在独立起源的自然种群中GD后反复发生的变化是否相同？ （3）相反，与该多倍体的一个形成到下一个形成的方面是否高度可变？为了解决这些问题，将构建二倍体T. dubius的核基因组序列并用作全基因组作为检测的参考。该基因组也将具有潜在的经济价值，因为Tragopogon与生菜密切相关，这是一个重要的农作物。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模式变化的基因紧密相关。