Context Dependency of Mutations in Chloroplast DNA

叶绿体 DNA 突变的背景依赖性

• 批准号: 9727906
• 负责人: Brian Morton
• 金额: $ 1.1万
• 依托单位: Barnard College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-01-01 至 2000-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9727906&HistoricalAwards=false
• 关键词: Context; Dependency; Mutations; Chloroplast; DNA

9727906 Morton The influence of context, or neighboring base composition, on the pattern and rate of nucleotide substitution in the chloroplast genome will be examined. Recent work has demonstrated a strong correlation between flanking base composition and both substitution rate and mutation bias in flowering plants. This interdependency of sites has important implications for processes as well as analyses in many fields of molecular biology. We are interested in further expanding our previous findings in order to develop a better understanding of how much variation in substitution bias and rate is a function of context as well as how context dependency affects mutation spectra and gene evolution. The proposed work focuses on the chloroplast genome and will analyze the influence of context on the rate of substitution with the goal of determining how context dependency - as opposed to natural selection - affects variation in substitution rate among genes. The influence of context on substitutions in species other than flowering plants will then be tested. Finally, the effect that observed context dependencies have on gene-level evolutionary features will be examined. This will include the effect on variation in synonymous substitution rate (mentioned above), how context dependency affects the dynamics of amino acid replacement and the influence of context dependency on frequently applied methods in molecular phylogenetics that assume an independence of sites. In addition to the direct applications, this work will also develop a strong basis for studies on other genomes and other groups of organisms as well as an understanding of mutation dynamics in this widely studied and analyzed genome.

环境或邻近碱基组成对叶绿体基因组中核苷酸取代的模式和速率的影响将被检验。最近的研究表明，开花植物的侧翼碱基组成与替代率和突变偏倚之间存在很强的相关性。这种位点的相互依赖性对分子生物学许多领域的过程和分析具有重要意义。我们有兴趣进一步扩展我们以前的发现，以便更好地理解替代偏差和比率的变化程度是上下文的函数，以及上下文依赖性如何影响突变谱和基因进化。拟议的工作侧重于叶绿体基因组，并将分析环境对替代率的影响，目的是确定环境依赖（与自然选择相反）如何影响基因间替代率的变化。然后将测试环境对开花植物以外物种的替代的影响。最后，观察到的环境依赖性对基因水平进化特征的影响将被检查。这将包括对同义取代率变化的影响（如上所述），上下文依赖如何影响氨基酸替代的动力学，以及上下文依赖对假设位点独立性的分子系统发育中常用方法的影响。除了直接应用外，这项工作还将为其他基因组和其他生物群体的研究以及对这一广泛研究和分析的基因组的突变动力学的理解奠定坚实的基础。