Variation of D. melanogaster chromosome 4

黑腹果蝇 4 号染色体变异

• 批准号: 6576815
• 负责人: Manyuan LONG
• 金额: $ 25.48万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-07-01 至 2007-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6576815
• 关键词: Drosophilidae; animal population genetics; arthropod genetics; chromatin; chromosomes; evolution; gene expression; genetic models; genetic polymorphism; genetic recombination; high performance liquid chromatography; northern blottings; nucleic acid sequence; polymerase chain reaction; statistics /biometry

DESCRIPTION (provided by applicant): The objective of this research is to study evolutionary forces that govern unusual variation of the D. melanogaster fourth chromosome uncovered recently by us. For a long time, this chromosome has been viewed as a canonical textbook example of how natural selection can result in low within-species variation in a genome region of low recombination. Our preliminary work has indicated that the previous conclusion that the entire chromosome 4 harbors low variation is incorrect and should not be taken as a paradigm any more. We have found a high level of nucleotide variation in large blocks of this chromosome in D. melanogaster and simulans. The following objectives will be pursued. (1) Using Monte Carlo simulations based on the coalescent process with selection and recombination, we will investigate a theoretical population genetic process associated with a low average recombination rate in the whole chromosome but with sporadic recombination hot spots. We expect that this theoretical analysis will shed new light on the relationship between recombination and variation. (2) To determine the length of the high variation region in the chromosome, we will characterize the polymorphism distribution in natural populations in whole euchromatin regions of the D. melanogaster fourth chromosome. (3) To compare the high variation region of D. melanogaster with the corresponding region in other sibling species, we will investigate sequence variation in D. simulans and D. yakuba. Finally, using these theoretical results and variation data, we will test several hypotheses that might explain the variation and evolution of the chromosome: selective sweep, background selection, balancing selection, and neutrality. We will also characterize the variation and evolution of the sphinx gene, a gene that recently originated on the D. melanogaster fourth chromosome, with structural and expression analysis, and investigate its potential role in the evolution of the chromosome. These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome.

描述（由申请人提供）：这项研究的目的是研究美国最近发现的D. melanogaster第四染色体的异常变化的进化力。 长期以来，该染色体一直被视为一个规范的教科书示例，说明自然选择如何导致低重组基因组区域的种类内部变化较低。我们的初步工作表明，先前的结论是，整个染色体4港口低变化是不正确的，不应再将其视为范式。我们发现在D. melanogaster和simulans中，该染色体大块的大块中有高水平的核苷酸变化。将实现以下目标。 （1）使用基于合并过程的蒙特卡洛模拟与选择和重组，我们将研究与整个染色体中平均重组率低相关的理论种群遗传过程，但与零星的重组热点有关。我们预计这种理论分析将为重组与变异之间的关系提供新的启示。 （2）为了确定染色体高变异区域的长度，我们将表征D. melanogaster四染色体的整个白染色质区域中自然种群中的多态性分布。 （3）将D. melanogaster的高变异区与其他兄弟姐妹物种中的相应区域进行比较，我们将研究D. simulans和D. Yakuba的序列变化。最后，使用这些理论结果和变异数据，我们将测试几种可能解释染色体变化和演变的假设：选择性扫描，背景选择，平衡选择和中立性。我们还将表征狮身人面基基因的变异和演变，该基因最近起源于D. melanogaster第四染色体，具有结构性和表达分析，并研究了其在染色体进化中的潜在作用。 这些研究应大大增加对果蝇第四染色体进化遗传学的理解。