Dynamics and determinants of copy number variation in evolving populations

DNA拷贝数变异是许多遗传性状差异的基础，并涉及从病原体的抗药性到动物驯化的不同过程。这项研究的目的是描述进化种群中拷贝数变化的动态，并了解促进其产生的基因组特性。利用实验室中的进化实验，该项目将研究随着种群在选择下的进化而产生的拷贝数变化的动态。该项目将使用一组突变体来测试产生拷贝数变化的不同过程的作用。这项研究的完成将为拷贝数变异的产生和选择提供重要的新见解，从而更全面地理解进化过程，并可能应用于微生物耐药性和工业微生物学。为了扩大科学培训活动的影响，这项研究将为来自传统上代表性不足的群体的本科生和高中生提供机会，在我们的实验室进行指导研究。此外，作为该项目的一部分，将完成一本免费提供的在线教科书，其中包括遗传学、统计学和计算机编程方面的教学。为了定量了解CNV在进化人口中的作用，该项目将使用新开发的CNV报告系统，该系统包含一个结构性表达的荧光蛋白基因，该基因与CNV被反复选择的位置相连。利用萌芽酵母(酿酒酵母)在营养受限的恒化器中的长期实验进化，该项目将使用CNV报告程序来量化三个具有不同基因组结构的基因座上CNV的进化动态。为了确定在每个进化群体中产生和选择的独特CNV的数量，该项目将使用一种血统跟踪方法，使用随机分子条形码和基于FACS的CNV谱系分离。通过对含有CNV的谱系进行下一代DNA测序，该项目将确定CNV形成的机制。该项目将利用DNA复制和修复组件的突变菌株来研究不同途径在CNV形成中的作用。为了测试不同序列元素的影响，该项目将改变这三个基因座的基因组结构，并测试对CNV动力学和多样性的影响。最后，该项目还将测试转录激活是否影响CNV形成率。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

DNA copy number variation underlies differences in many inherited traits and is involved in diverse processes ranging from drug resistance in pathogens to domestication of animals. The study aims to characterize the dynamics of copy number variation in evolving populations and to understand the properties of the genome that facilitate their generation. Using evolution experiments in the lab, the project will investigate the dynamics with which copy number variation arises as populations evolve under selection. The project will test the role of different processes that generate copy number variation using a panel of mutants. Completion of this study will provide important new insights into the generation and selection of copy number variation leading to a more complete understanding of evolutionary processes with potential applications to microbial drug resistance and industrial microbiology. To broaden the impact of the scientific training activities, the study will provide opportunities for undergraduate and high school students from traditionally under-represented groups to undertake mentored research in our laboratory. In addition, a freely available, online textbook integrating instruction in genetics, statistics and computer programming will be completed as part of the project. To gain quantitative insights into the role of CNVs in evolving populations, the project will use a newly developed CNV reporter system that comprises a constitutively expressed fluorescent protein gene linked to loci at which CNVs are recurrently selected. Using long term experimental evolution of budding yeast (Saccharomyces cerevisiae) in nutrient-limited chemostats, the project will use the CNV reporter to quantify the evolutionary dynamics of CNVs at three loci that have distinct genomic architectures. To identify the number of unique CNVs that are generated and selected in each evolving population, the project will employ a lineage tracking method using random molecular barcodes and FACS-based isolation of CNV-containing lineages. Using next generation DNA sequencing of lineages containing CNVs, the project will define the mechanisms by which CNVs are formed. The project will study the role of different pathways on CNV formation using strains mutant for DNA replication and repair components. To test the effect of different sequence elements the project will alter the genomic architecture of the three loci and test the effect on CNV dynamics and diversity. Finally, the project will also test whether transcriptional activation impacts CNV formation rates.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.