Chloroplast genome sequence data is very useful in studying/addressing the phylogeny of plants at various taxonomic ranks. However, there are no empirical observations on the patterns, directions, and mutation rates, which are the key topics in chloroplast genome evolution. In this study, we used Calycanthaceae as a model to investigate the evolutionary patterns, directions and rates of both nucleotide substitutions and structural mutations at different taxonomic ranks. There were 2861 polymorphic nucleotide sites on the five chloroplast genomes, and 98% of polymorphic sites were biallelic. There was a single-nucleotide substitution bias in chloroplast genomes. A → T or T → A (2.84%) and G → C or C → G (3.65%) were found to occur significantly less frequently than the other four transversion mutation types. Synonymous mutations kept balanced pace with nonsynonymous mutations, whereas biased directions appeared between transition and transversion mutations and among transversion mutations. Of the structural mutations, indels and repeats had obvious directions, but microsatellites and inversions were non-directional. Structural mutations increased the single nucleotide mutations rates. The mutation rates per site per year were estimated to be 0.14–0.34 × 10− 9 for nucleotide substitution at different taxonomic ranks, 0.64 × 10− 11 for indels and 1.0 × 10− 11 for repeats. Our direct counts of chloroplast genome evolution events provide raw data for correctly modeling the evolution of sequence data for phylogenetic inferences.

中文翻译：

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花蕾科叶绿体基因组中单核苷酸取代和结构突变的进化方向。


叶绿体基因组序列数据对于研究/解决不同分类等级植物的系统发育非常有用。然而，对于叶绿体基因组进化的关键主题——模式、方向和突变率，还没有实证观察。在本研究中，我们以蜡梅科为模型，研究不同分类等级的核苷酸取代和结构突变的进化模式、方向和速率。 5个叶绿体基因组上共有2861个多态性核苷酸位点，其中98%的多态性位点是双等位的。叶绿体基因组中存在单核苷酸替换偏差。 A → T 或 T → A (2.84%) 和 G → C 或 C → G (3.65%) 的发生频率明显低于其他四种颠换突变类型。同义突变与非同义突变保持平衡的步伐，而转换突变和颠换突变之间以及颠换突变之间则出现有偏差的方向。结构突变中，插入缺失和重复有明显的方向性，而微卫星和倒位则无方向性。结构突变增加了单核苷酸突变率。对于不同分类等级的核苷酸替换，每年每个位点的突变率估计为 0.14–0.34 × 10− 9，插入缺失为 0.64 × 10− 11，重复为 1.0 × 10− 11。我们对叶绿体基因组进化事件的直接计数为正确建模序列数据的进化以进行系统发育推断提供了原始数据。