Evolutionary and functional consequences of structural genetic variation in Drosophila

果蝇结构遗传变异的进化和功能后果

• 批准号: 10369357
• 负责人: MAHUL CHAKRABORTY
• 金额: $ 4.49万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-01 至 2021-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10369357
• 关键词: Affect; Animal Model; Biological Assay; Biological Process; Biological Sciences; CRISPR/Cas technology; California; Catalogs; Classification; Complement; Complex; Data; Development; Disease; Drosophila genus; Drosophila melanogaster; Engineering; Ensure; Frequencies; Gene Duplication; Generations; Genetic; Genetic Polymorphism; Genetic Structures; Genetic Variation; Genome; Genome engineering; Genomic Segment; Genotype; Grant; Heritability; Human; Human Genome; Individual; Link; Malignant Neoplasms; Maps; Measures; Mendelian disorder; Methods; Molecular; Mutation; Natural Selections; Nicotine; Organism; Other Genetics; Oxidative Stress; Pattern; Pesticides; Phase; Phenotype; Platinum; Polymorphism Analysis; Population Genetics; Positioning Attribute; Proxy; Research; Resistance; Resources; SNP array; Sampling Biases; Schizophrenia; Series; Site; Source; Structure; Training; Universities; Variant; base; career; causal variant; disease phenotype; experience; fitness; genome editing; genome-wide; human disease; reference genome; response; structural genomics; theories; thermal stress; tool; trait

PROJECT SUMMARY Genomic structural variants (SV) involving deletions, duplications, insertions, inversions, and translocations of sequences are an abundant source of genetic variation. SVs have been linked to Mendelian diseases, as well as complex heritable diseases like schizophrenia, and cancer. However, recent comparisons of extremely contiguous genome assemblies of humans and model organism Drosophila melanogaster have revealed that common genotyping strategies relying on high throughput short reads miss 40-80% of SVs, including those affecting phenotypes. Thus, contribution of SVs towards diseases and phenotypic variation remain grossly underestimated. To accurately measure the contribution of SVs towards deleterious genetic variation and trait variation, we propose to create a comprehensive map of genomewide SVs via comparison of extremely contiguous genome assemblies. However, contiguous de novo assembly of human genomes with high coverage (>50X) noisy long reads remains prohibitively expensive. So I propose to analyze SVs in the 25-fold smaller genome of model organism D. melanogaster, which has contributed substantially to our understanding of the genetics of complex human diseases. The proposed research aims to study fitness effects of polymorphic SVs based on de novo genome assemblies of 50 genetically diverse D. melanogaster strains that are as complete and contiguous as the current D. melanogaster reference genome – arguably the best metazoan genome assembly (Aim 1). I propose to use this comprehensive set of variants to infer the distribution of fitness effects of the SVs and to estimate the proportion of adaptive SVs, both of which are reliable proxies for the evolutionary and functional significance of SVs (Aim 1). Aim 1 will involve training in theory and cutting edge methods in molecular population genetics. Next, the proposed project will develop an experimental approach to determine the fitness effects of variants for which an organismal phenotype is unknown. As part of this, the proposed project will develop genome editing resources that will facilitate rapid transformation of one of our sequenced strains with SVs, so that fitness effects of candidate SVs from trait mapping studies can be examined (Aim 2). Training in Aim 2 includes development of CRISPR-Cas9 toolkit in a common genetic background to investigate the functional effects of SVs. Finally, using the toolkit developed in Aim 2, we propose to conduct high throughput fitness assays to evaluate the selective effects of SVs under specific selection conditions (Aim 3). The training portion of the proposed research will complement the applicant’s previous experience and position him for a successful research career. University of California Irvine and the Emerson and Long labs together have the resources and expertise to ensure the successful completion of the training phase of the grant.

项目摘要 基因组结构变异体（SV），涉及缺失、重复、插入、倒位和易位， 序列是遗传变异的丰富来源。SV也与孟德尔疾病有关 像精神分裂症和癌症这样复杂的遗传性疾病。然而，最近的比较， 人类和模式生物黑腹果蝇的连续基因组组装揭示， 依赖于高通量短读段的常见基因分型策略错过了40-80%的SV，包括那些 影响表型。因此，SV对疾病和表型变异的贡献仍然很大， 低估为了准确测量SV对有害遗传变异和性状的贡献， 变异，我们建议通过比较极端的 连续的基因组组装。然而，具有高表达的人类基因组的连续从头组装， 覆盖率（> 50 X）的噪声长读段仍然非常昂贵。所以我建议分析25倍的SV 模式生物D.黑腹菌，它对我们理解 复杂的人类疾病的遗传学。拟议的研究旨在研究健身效果， 多态性SV基于50个遗传多样性D.黑腹菌菌株， 和现在的D一样完整和连续黑腹参考基因组-可以说是最好的 后生动物基因组组装（Aim 1）。我建议使用这套全面的变体来推断 分布的适应性影响的SV和估计的比例，自适应SV，这两者都是 SV进化和功能重要性的可靠代表（目标1）。目标1将涉及以下方面的培训： 分子群体遗传学的理论和前沿方法。下一步，拟议项目将开发一个 实验方法，以确定适应性的影响，其中一个有机体表型的变异， 未知作为其中的一部分，拟议的项目将开发基因组编辑资源， 用SV转化我们的一个测序菌株，使来自性状的候选SV的适应性效应 可以审查绘图研究（目标2）。目标2的培训包括开发CRISPR-Cas9工具包， 一个共同的遗传背景，调查SV的功能影响。最后，使用开发的工具包 在目标2中，我们建议进行高通量适应性测定，以评估SV在以下条件下的选择效果： 具体选择条件（目标3）。拟议研究的培训部分将补充 申请人以前的经验，并定位他为一个成功的研究生涯。加州大学 Irvine与Emerson和Long实验室共同拥有资源和专业知识， 完成赠款的培训阶段。