Context Dependency of Mutations in Chloroplast DNA

小行星9727906 上下文的影响，或相邻的碱基组成，在叶绿体基因组中的核苷酸取代的模式和速率将被检查。 最近的工作已经证明了显花植物中侧翼碱基组成与取代率和突变偏好之间的强相关性。 位点的这种相互依赖性对分子生物学的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大我们以前的研究结果，以更好地了解有多少变化的替代偏差和速率是一个功能的背景，以及如何上下文依赖性影响突变谱和基因进化。 拟议的工作重点是叶绿体基因组，并将分析背景对替代率的影响，目标是确定背景依赖性-而不是自然选择-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的物种中的替换的影响。 最后，观察到的上下文依赖性对基因水平的进化特征的影响将被检查。 这将包括对同义替换率变化的影响（如上所述），背景依赖性如何影响氨基酸替换的动力学，以及背景依赖性对分子遗传学中假设位点独立性的常用方法的影响。 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奠定坚实的基础，并了解这一广泛研究和分析的基因组中的突变动态。

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.