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Structural variation population size and the evolution of genome complexity

结构变异种群规模和基因组复杂性的进化

基本信息

批准号：
10216301
负责人：
James Jordan Emerson
金额：
$ 30.62万
依托单位：
UNIVERSITY OF CALIFORNIA-IRVINE
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-08-01 至 2023-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10216301
关键词：
Address Affect Animals Automobile Driving Cancer Etiology Chromosomes Collection Complex DNA Data Disease Drosophila genus Effectiveness Environment Evolution Exhibits Gene Expression Gene Frequency Gene Structure Genes Genetic Genetic Diseases Genetic Drift Genetic Polymorphism Genetic Transcription Genetic Variation Genome Genomics Genotype Goals Health Human Human Genetics Individual Lead Link Maintenance Malignant Neoplasms Maps Mutation Natural Selections Neighborhoods Nucleic Acid Regulatory Sequences Organism Pattern Personal Satisfaction Phase Phenotype Plants Platinum Play Population Population Genetics Population Sizes Recording of previous events Resistance Resolution Role Sampling Source Structure Testing Variant Work base comparative genomics driving force fitness genome resource genome-wide genomic variation innovation mutant pathogen pesticide resistance preservation reference genome sample fixation

项目摘要

Project Summary The primary goal for this proposal is to determine how mutations that change genome structure (e.g. duplications or deletions of sections of chromosomes) are acquired and preserved. To accomplish this, the evolutionary forces that govern the fate of such mutations will be inferred by sequencing populations within several species groups of Drosophila. Structural variation is an important source of genetic novelty and is thought to play an important role in the origin of genetic complexity. A general understanding of structural variation is important because it plays major roles in the etiology of cancer, the emergence of pathogen resistance, and the origin of pesticide resistance for plant and animal crop pests, among many other topics of relevance to human health and well-being. The project will be executed by studying genomic variation in pairs of closely related Drosophila species. In order to disentangle the influence of genetic drift and natural selection, genome-wide sequencing data for species pairs that exhibit large differences in their population sizes will be collected. This approach works because, as populations become smaller, genetic drift dominates genetic variation more and more. Conversely, as populations become larger, genetic drift's influence on genetic variation becomes weaker and weaker. Thus, it is predicted that, when natural selection drives the acquisition and maintenance of structural mutations, larger populations will acquire and maintain more variants than smaller ones. However, if genetic drift is the major factor, then smaller populations acquire and maintain more variants than larger ones. The project is split into three major phases. The first is collection of and assembly of reference genome data for each species, which will be done using long molecule sequencing strategies. The second is collection of population sequencing data for use in genotyping structural variants. The final phase is to combine genotype and gene annotations and subject them to evolutionary analysis to address the questions proposed above.

项目摘要该提案的主要目标是确定如何改变基因组结构的突变（例如，染色体片段的重复或缺失）被获取并保存。为了实现这一点，控制这些突变命运的进化力量将通过对这些突变中的种群进行测序来推断。果蝇的几个种群。结构变异是遗传新奇的重要来源，被认为在遗传复杂性的起源中起着重要作用。对结构的一般理解变异是重要的，因为它在癌症的病因学、病原体的出现、抗性，以及植物和动物作物害虫的杀虫剂抗性起源，以及许多其他主题，与人类健康和福祉的相关性。该项目将通过研究密切相关的果蝇物种对的基因组变异来执行。在为了解开遗传漂变和自然选择的影响，将收集种群规模差异较大的物种对。这种方法是有效的因为，随着种群变小，遗传漂变越来越多地支配着遗传变异。相反地，随着种群规模的扩大，遗传漂变对遗传变异的影响越来越小。因此，在本发明中，据预测，当自然选择驱动结构突变的获得和维持时，较大的种群将比较小的种群获得和保持更多的变异。然而，如果遗传漂变是主要因素，那么较小的群体比较大的群体获得并保持更多的变异。该项目分为三个主要阶段。第一个是收集和组装参考基因组数据，每个物种，这将使用长分子测序策略来完成。第二是收集用于基因分型结构变体的群体测序数据。最后阶段是将联合收割机基因型和基因注释，并对其进行进化分析，以解决上述问题。

项目成果

期刊论文数量（5）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila.

DOI：
10.1101/gr.266130.120
发表时间：
2021-03
期刊：
Genome research
影响因子：
7
作者：
Liao Y;Zhang X;Chakraborty M;Emerson JJ
通讯作者：
Emerson JJ

Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies.

DOI：
10.1073/pnas.2301411120
发表时间：
2023-08-15
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
影响因子：
11.1
作者：
Chakraborty, Mahul;Lara, Angelica Guadalupe;Dang, Andrew;McCulloch, Kyle J.;Rainbow, Dylan;Carter, David;Ngo, Luna Thanh;Solares, Edwin;Said, Iskander;Corbett-Detig, Russell B.;Gilbert, Lawrence E.;Emerson, J. J.;Briscoe, Adriana D.
通讯作者：
Briscoe, Adriana D.

Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish.