DISSERTATION RESEARCH: Developing a toolbox for evolutionary inferences in polyploids: new methods of analysis applied to the plant genus Penstemon (Plantaginaceae)

论文研究：开发多倍体进化推理工具箱：应用于植物属 Penstemon（车前草科）的新分析方法

• 批准号: 1601096
• 负责人: Andrea Wolfe
• 金额: $ 2万
• 依托单位: Ohio State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2018-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1601096&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; Developing; toolbox; evolutionary

Whole genome duplication, or polyploidy, is a common phenomenon in many plants wherein all chromosomes are doubled. A major challenge for working with species with duplicated genomes is that the extra gene copies make it extremely difficult to reconstruct their evolutionary relationships. The goal of this project is to develop and apply new statistical tools that take advantage of modern DNA sequencing technologies to enable the study of polyploid organisms. These tools will then be used to study patterns of hybridization and whole genome duplication in a complex group of polyploids in beardtongues, plants from the genus Penstemon. In addition to providing opportunities for graduate student training in laboratory and bioinformatics techniques, this project will produce and freely distribute software code for use by evolutionary biologists. Although polyploidy has played an important role in the history of many eukaryotic lineages, there are few tools for studying and understanding their genetic history at contemporary timescales. Two of the main reasons for this are (1) ambiguous genotypes due to uncertainty in allele copy number and (2) complex patterns of allelic inheritance that can vary at different loci across the genome. The proposed work addresses these issues by developing a statistical framework to infer inheritance patterns from high throughput sequencing data while simultaneously accounting for genotype uncertainty. It will develop a model that will then be used to test hypotheses regarding the origins of the allohexaploid Penstemon attenuatus species complex, which contains four regional varieties each with different putative parental species. Double digest restriction site associated DNA sequencing will be employed to gather genome-wide Single Nucleotide Polymorphism (SNP) data for the model, and hypotheses of allopolyploid origin will be evaluated using tests for introgression. The statistical model will facilitate the study of polyploidy in other non-model organisms.

在许多植物中，整个基因组重复或多倍体是一种常见现象，其中所有染色体都会加倍。与具有重复基因组的物种一起工作的一个主要挑战是，额外的基因副本使重建其进化关系变得极为困难。该项目的目的是开发和应用新的统计工具，以利用现代DNA测序技术来研究多倍体生物。然后，这些工具将用于研究Beardtongues的复杂多倍体（来自Penstemon属的植物）中杂交和整个基因组重复的模式。除了为实验室和生物信息学技术的研究生培训提供机会外，该项目还将生产并自由分发软件代码，以供进化生物学家使用。尽管多倍体在许多真核谱系的历史中发挥了重要作用，但很少有工具可以研究和了解其在当代时代标准的遗传史。造成这种情况的两个主要原因是（1）由于等位基因拷贝数的不确定性以及（2）在基因组中不同基因座变化的等位基因遗传模式而导致的歧义基因型。提出的工作通过开发一个统计框架来解决这些问题，从高吞吐量测序数据中推断出继承模式，同时考虑基因型不确定性。它将开发一个模型，然后将用于测试有关Allohexaploid Penstemon Attenuatus物种综合体的起源的假设，该物种包含四个区域性品种，每个品种各有不同的父母种类。将采用双消化限制位点相关的DNA测序来收集模型全基因组的单核苷酸多态性（SNP）数据，并将使用into int intosression测试来评估异倍倍体原点的假设。统计模型将促进其他非模型生物中多倍体的研究。