Genomic Mechanisms of Chromosomal Rearrangements in Drosophila Pseudoobscura

描述(由申请人提供)： 当个体出现遗传病的症状时，通常会在人类身上检测到染色体倒置。有两个不同倒位的个体可能生育能力较低，因为倒染色体之间的基因交换可以导致精子或卵子的形成，遗传信息或多或少都有。然而，反转也可以在种群中出现，频率很高，对生存或繁殖没有明显的负面影响。这项提议将检验关于反转如何在人群中产生、传播和维持的假说。拟黑腹果蝇是研究倒位的一个模式系统，因为它的第三条染色体对种群中30多种不同的基因排列是多态的。这些排列是通过一系列重叠的着丝粒旁倒置产生的。逆温频率在形成倾斜或梯度的种群中有所不同，其主要频率漂移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，并呈现高度倾斜性。实验室的种群笼实验表明，不同的基因排列保持在稳定的平衡频率。这项研究将使用下一代技术对携带六种主要染色体排列之一的50株假黑线菌进行重新测序。下一代基因序列分析将用于量化果蝇幼虫和成虫两个不同生活阶段的六个不同倒位背景之间的表达差异。重新测序的数据将识别倒位断点序列，并改进假黑斑潜蝇基因组组装。转录组数据将被用来改进假黑斑潜蝇基因模型的注释。对核苷酸多态和基因表达数据的分子群体遗传学分析将检验关于新倒位如何在群体中传播的四类假说：(1)由于重组减少而导致的间接影响，导致染色体没有有害突变或增强适应基因的链接；(2)修复欠显性排列的遗传漂移；(3)染色体损伤的直接影响，如基因结构或表达的改变；或(4)与适应等位基因的遗传搭便车。这些分析将检验关于反转如何在种群中保持的两个假说：(1)超显性；或(2)作为一种受保护的多态。显示差异表达或蛋白质变异的基因可能会在未来的实验中被操纵，这些实验旨在了解支撑倒置进化的分子遗传学基础。

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.