Dettman Jeremy R, Sztepanacz Jacqueline L, Kassen Rees
Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
BMC Genomics. 2016 Jan 5;17:27. doi: 10.1186/s12864-015-2244-3.
Natural genetic variation ultimately arises from the process of mutation. Knowledge of how the raw material for evolution is produced is necessary for a full understanding of several fundamental evolutionary concepts. We performed a mutation accumulation experiment with wild-type and mismatch-repair deficient, mutator lines of the pathogenic bacterium Pseudomonas aeruginosa, and used whole-genome sequencing to reveal the genome-wide rate, spectrum, distribution, leading/lagging bias, and context-dependency of spontaneous mutations.
Wild-type base-pair mutation and indel rates were ~10(-10) and ~10(-11) per nucleotide per generation, respectively, and deficiencies in the mismatch-repair system caused rates to increase by over two orders of magnitude. A universal bias towards AT was observed in wild-type lines, but was reversed in mutator lines to a bias towards GC. Biases for which types of mutations occurred during replication of the leading versus lagging strand were detected reciprocally in both replichores. The distribution of mutations along the chromosome was non-random, with peaks near the terminus of replication and at positions intermediate to the replication origin and terminus. A similar distribution bias was observed along the chromosome in natural populations of P. aeruginosa. Site-specific mutation rates were higher when the focal nucleotide was immediately flanked by C:G pairings.
Whole-genome sequencing of mutation accumulation lines allowed the comprehensive identification of mutations and revealed what factors of molecular and genomic architecture affect the mutational process. Our study provides a more complete view of how several mechanisms of mutation, mutation repair, and bias act simultaneously to produce the raw material for evolution.
自然遗传变异最终源于突变过程。全面理解几个基本的进化概念需要了解进化原材料是如何产生的。我们对野生型和错配修复缺陷型的病原菌铜绿假单胞菌突变株系进行了突变积累实验，并利用全基因组测序来揭示全基因组范围内自发突变的速率、谱、分布、前导链/后随链偏向性以及上下文依赖性。
野生型碱基对突变率和插入缺失率分别约为每代每个核苷酸10^(-10)和10^(-11)，错配修复系统缺陷导致这些速率增加了两个多数量级。在野生型株系中观察到普遍的向AT的偏向性，但在突变株系中则反转成向GC的偏向性。在前导链与后随链复制过程中发生的各类突变的偏向性在两个复制叉中相互检测到。突变沿染色体的分布是非随机的，在复制终点附近以及复制起点与终点之间的位置出现峰值。在铜绿假单胞菌自然种群的染色体上也观察到类似的分布偏向性。当焦点核苷酸紧邻C:G配对时，位点特异性突变率更高。
突变积累株系的全基因组测序能够全面鉴定突变，并揭示分子和基因组结构的哪些因素影响突变过程。我们的研究提供了一个更完整的视角，即突变、突变修复和偏向性的几种机制如何同时作用以产生进化的原材料。
