Evolutionary and functional consequences of structural genetic variation in Drosophila

项目总结 涉及基因缺失、重复、插入、倒置和易位的基因组结构变异(SV) 序列是遗传变异的丰富来源。SVS也与孟德尔疾病有关 作为复杂的遗传性疾病，如精神分裂症和癌症。然而，最近的对比显示， 人类和模式生物黑腹果蝇的连续基因组组合揭示了 依赖于高通量短读的常见基因分型策略遗漏了40%-80%的SVS，包括 影响表型的。因此，SVS对疾病和表型变异的贡献仍然很大。 被低估了。准确测量SVS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SVS来创建全基因组SVS的全面图谱 相邻的基因组组装。然而，人类基因组的连续从头组装具有高 覆盖范围(&gt；50X)噪声较大的长读取仍然昂贵得令人望而却步。因此我建议将SVS分析为25倍 更小的基因组，这对我们的理解有很大贡献 复杂的人类疾病的遗传学。这项拟议的研究旨在研究健身的影响 基于50个遗传多样性的黑腹葡萄球菌菌株的从头基因组组装的多态SVS 与目前的黑腹葡萄球菌参考基因组一样完整和连续--可以说是最好的 后生动物基因组组装(目标1)。我建议使用这组全面的变种来推断 支持向量机的适应度分布和估计自适应支持向量机的比例，两者都是 SVS进化和功能意义的可靠指标(目标1)。目标1将包括培训 分子群体遗传学的理论和前沿方法。下一步，拟议的项目将开发一个 确定某一生物表型的变异体适合度效应的实验方法 未知。作为这项工作的一部分，拟议的项目将开发基因组编辑资源，以促进快速 用SVS对我们测序的一个菌株进行转化，使候选SVS从性状上的适应度效应 可以审查测绘研究(目标2)。AIM 2培训包括开发CRISPR-CAS9工具包 一个共同的遗传背景来研究SVS的功能效应。最后，使用所开发的工具包 在目标2中，我们建议进行高通量适应度分析来评估支持向量机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，并为他的研究事业的成功奠定基础。加州大学 欧文、艾默生和Long实验室共同拥有资源和专业知识，确保成功 完成赠款的培训阶段。

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.