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: 10729933
• 负责人: MAHUL CHAKRABORTY
• 金额: $ 24.9万
• 依托单位: TEXAS A&M UNIVERSITY
• 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 2025-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10729933
• 关键词: Affect; Biological Assay; Biological Process; Biological Sciences; CRISPR/Cas technology; California; Catalogs; Categories; Classification; Complement; Complex; Data; Development; Disease; Drosophila genus; Drosophila melanogaster; Engineering; Ensure; Frequencies; Gene Duplication; Generations; Genetic; Genetic Polymorphism; Genetic Variation; Genome; Genome engineering; Genomic Segment; Genomics; Genotype; Grant; Heritability; Human; Human Genome; Individual; Link; Malignant Neoplasms; Maps; Measures; Mendelian disorder; Methods; Modeling; Molecular; Mutation; Natural Selections; Nicotine; Organism; Other Genetics; Oxidative Stress; Pattern; Pesticides; Phase; Phenotype; Platinum; Population Genetics; Positioning Attribute; Proxy; Research; Resistance; Resources; SNP array; Sampling Biases; Schizophrenia; Series; Site; Source; Structure; Training; Universities; Variant; career; causal variant; experience; fitness; genome editing; genome-wide; human disease; model organism; reference genome; response; 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 基因组结构变体（SV），涉及缺失，重复，插入，反转和易位 SV也与孟德尔疾病有关 作为精神分裂症和癌症等复杂的遗传疾病。但是，最近的比较 人类的连续基因组组件和模型有机体果蝇曲目揭示了 依靠高吞吐量短读数的常见基因分型策略错过了40-80％的SV，包括 影响表型。这是SVS对疾病和表型变异的贡献仍然严重 被低估了。准确测量SV对有害遗传变异和性状的贡献 变化，我们建议通过比较极端 连续的基因组组件。然而，人类基因组的连续de从头组装高 覆盖范围（> 50倍）的噪音长读数仍然昂贵。因此，我建议分析25倍的SVS 模型有机体的较小基因组D. Melanogaster，这为我们的理解做出了重大贡献 复杂人类疾病的遗传学。拟议的研究旨在研究适应性的影响 基于从头开始的基因组组件的多态性SVS，该基因组的基因组组件是50种遗传学的D. melanogaster Strewns 与当前的D. melanogaster参考基因组一样完整和连续 - 可以说是最好的 后生基因组组装（AIM 1）。我建议使用这组全面的变体来推断 SVS的适应性效应的分布并估算自适应SV的比例，这两个都是 SVS的进化和功能意义的可靠代理（AIM 1）。 AIM 1将涉及培训 分子种群遗传学中​​的理论和尖端方法。接下来，拟议的项目将开发 确定有机表型的变体的适应性影响的实验方法 未知。作为此的一部分，拟议的项目将开发基因组编辑资源，以促进快速 使用SVS的测序菌株之一转换，因此特征的候选SV的适应性影响 可以检查映射研究（AIM 2）。 AIM 2中的培训包括开发CRISPR-CAS9工具包 研究SV的功能效应的常见遗传背景。最后，使用工具包开发了 在AIM 2中，我们提议进行高吞吐量适应性评估，以评估SV的选择性影响 特定的选择条件（目标3）。拟议研究的培训部分将完成 申请人以前的经验，并将他定位为成功的研究职业。加利福尼亚大学 欧文（Irvine）和艾默生（Emerson）和长实验室共同拥有资源和专业知识，以确保成功 赠款的培训阶段的完成。