Context Dependency of Mutations in Chloroplast DNA

9727906 Morton将研究上下文或邻近碱基组成对叶绿体基因组中核苷酸替换模式和速率的影响。最近的工作表明，侧翼碱基组成与开花植物的替换率和突变偏向之间存在很强的相关性。这种位点的相互依赖对分子生物学的许多领域的过程和分析都有重要的影响。我们有兴趣进一步扩展我们之前的发现，以便更好地理解替换偏差和替换比率的变化在多大程度上是上下文的函数，以及上下文依赖如何影响突变谱和基因进化。这项拟议的工作重点放在叶绿体基因组上，并将分析上下文对替换率的影响，目的是确定上下文依赖--而不是自然选择--如何影响基因间替换率的差异。然后将测试环境对开花植物以外物种替换的影响。最后，我们将考察观察到的语境依赖对基因水平进化特征的影响。这将包括对同义替换率变异的影响(如上所述)，上下文依赖如何影响氨基酸替换的动力学，以及上下文依赖对分子系统学中假设位点独立的常用方法的影响。除了直接应用外，这项工作还将为研究其他基因组和其他生物群以及了解这个被广泛研究和分析的基因组中的突变动力学奠定坚实的基础。

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.