Sloan Daniel B, Wu Zhiqiang
Department of Biology, Colorado State University, Fort Collins
Department of Biology, Colorado State University, Fort Collins.
Genome Biol Evol. 2014 Nov 21;6(12):3210-21. doi: 10.1093/gbe/evu253.
Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA (mtpts). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.
被子植物线粒体基因组具有许多不寻常的特性，包括核苷酸组成不均一以及基因组大小异常大且变化多样。确定诸如突变偏向等非适应性机制在塑造这些独特基因组的分子进化过程中的作用已被证明具有挑战性，因为它们的动态结构通常阻碍了用于比较分析的同源基因间序列的识别。在此，我们报告了对源自插入的质体DNA（mtpts）的被子植物线粒体DNA序列的分析。大量已完全测序的质体基因组的可得性使我们能够推断这些插入序列的进化历史，包括由于它们整合到线粒体基因组中而发生的特定核苷酸替换和插入缺失。我们的分析证实，许多mtpts具有复杂的历史，包括频繁的基因转换以及不同被子植物谱系之间水平转移的多个实例。然而，很明显，被子植物中现存的大多数mtpt序列是近期转移（或基因转换）的产物，并且容易快速丢失/退化，这表明大多数mtpts在进化过程中相对不受功能限制。mtpt序列的进化揭示了被子植物线粒体基因组中偏向性突变输入的模式，包括小缺失多于插入以及偏向于增加AT含量的核苷酸替换。然而，这些突变偏向远比在许多其他细胞基因组中观察到的要弱，这为被子植物线粒体结构的一些显著特征提供了见解，包括大基因间区域的保留以及这些区域中相对中性的GC含量。
