Genomic Mechanisms of Chromosomal Rearrangements in Drosophila Pseudoobscura

描述（由申请人提供）： 当个体出现遗传疾病的症状时，经常在人类中检测到染色体倒位。具有两种不同倒位的个体可能具有较低的生育力，因为倒位染色体之间的遗传交换可能导致形成具有较少或较多遗传信息的精子或卵子。然而，倒位也可以以高频率存在于种群中，对生存能力或繁殖没有明显的负面影响。这个提议将检验关于倒位如何在种群中产生、传播和维持的假设。 拟暗果蝇（Drosophila pseudobscura）是研究倒位的模式系统，因为它的第三条染色体在种群中具有超过30种不同基因排列的多态性。这些排列是通过一系列重叠的近着丝粒倒位产生的。反转频率在形成渐变或梯度的种群之间变化，其主要频率变化发生在美国西南部的主要气候带。基因排列频率随季节变化呈周期性变化，并有海拔梯度。实验室的群体笼实验表明，不同的基因排列保持在稳定的平衡频率。 本研究将使用新一代技术对50株D.携带六种主要染色体排列之一的假暗细胞。下一代mRNA测序分析将用于量化两个不同果蝇生命阶段（幼虫和成虫）的六种不同倒位背景之间的表达差异。重测序数据将鉴定倒位断裂点序列并改进D。拟暗细胞基因组组装。转录组数据将用于改进D.伪暗对核苷酸多态性和基因表达数据的分子群体遗传分析将检验关于新倒位如何在群体中传播的四类假设：（1）由于减少重组导致染色体无有害突变或增强适应性基因的连锁而产生的间接效应;（2）固定弱显性排列的遗传漂变;（3）染色体病变的直接影响，如基因结构或表达的改变;或（4）与适应性等位基因的遗传搭便车。这些分析将检验关于倒位如何在群体中维持的两个假设：（1）通过超显性;或（2）作为受保护的多态性。显示差异表达或蛋白质变异的基因可能在未来的实验中被操纵，这些实验旨在了解支持倒位进化的分子遗传基础。

DESCRIPTION (provided by applicant): Chromosomal inversions are often detected in humans when individuals present symptoms of genetic diseases. Individuals with two different inversions can have lower fertility because genetic exchange between inverted chromosomes can lead to the formation of sperm or eggs with less or more genetic information. Inversions, however, can also be present in populations at high frequencies with no apparent negative effects on viability or reproduction. This proposal will test hypotheses about how inversions arise, spread, and are maintained in populations. Drosophila pseudoobscura is a model system for the study of inversions because its third chromosome is polymorphic for over 30 different gene arrangements in populations. These arrangements were generated through a series of overlapping paracentric inversions. The inversion frequencies vary among populations forming clines or gradients whose major frequency shifts occur with major climatic zones in the southwestern United States. The gene arrangement frequencies cycle with the seasons and show altitudinal clines. Population cage experiments in the laboratory have shown that different gene arrangements are maintained at stable equilibrium frequencies. This study will use next generation technologies to re-sequence 50 strains of D. pseudoobscura that carry one of six major chromosomal arrangements. Next generation sequencing analysis of mRNA will be used to quantify expression differences among the six different inversion backgrounds for two different Drosophila life stages, larvae and adults. The re-sequencing data will identify inversion breakpoint sequences and improve the D. pseudoobscura genome assembly. The transcriptome data will be used to improve the annotation of gene models in D. pseudoobscura. Molecular population genetic analyses of nucleotide polymorphism and gene expression data will test four classes of hypotheses about how a new inversion spreads through a population: (1) indirect effects due to reduced recombination leading to chromosomes free of deleterious mutations or enhancing the linkage of adaptive genes; (2) genetic drift that fixes underdominant arrangements; (3) direct effects of the chromosomal lesion such as alteration of gene structure or expression; or (4) genetic hitchhiking with an adaptive allele. These analyses will test two hypotheses about how inversions are maintained in populations: (1) by overdominance; or (2) as a protected polymorphism. Genes that show differential expression or protein variation may be manipulated in future experiments designed to understand the molecular genetic basis that underpins inversion evolution.