Department of Biology, University of Virginia, VA, USA.
Genome Biol Evol. 2012;4(3):294-306. doi: 10.1093/gbe/evs006. Epub 2012 Jan 12.
The angiosperm genus Silene exhibits some of the most extreme and rapid divergence ever identified in mitochondrial genome architecture and nucleotide substitution rates. These patterns have been considered mitochondrial specific based on the absence of correlated changes in the small number of available nuclear and plastid gene sequences. To better assess the relationship between mitochondrial and plastid evolution, we sequenced the plastid genomes from four Silene species with fully sequenced mitochondrial genomes. We found that two species with fast-evolving mitochondrial genomes, S. noctiflora and S. conica, also exhibit accelerated rates of sequence and structural evolution in their plastid genomes. The nature of these changes, however, is markedly different from those in the mitochondrial genome. For example, in contrast to the mitochondrial pattern, which appears to be genome wide and mutationally driven, the plastid substitution rate accelerations are restricted to a subset of genes and preferentially affect nonsynonymous sites, indicating that altered selection pressures are acting on specific plastid-encoded functions in these species. Indeed, some plastid genes in S. noctiflora and S. conica show strong evidence of positive selection. In contrast, two species with more slowly evolving mitochondrial genomes, S. latifolia and S. vulgaris, have correspondingly low rates of nucleotide substitution in plastid genes as well as a plastid genome structure that has remained essentially unchanged since the origin of angiosperms. These results raise the possibility that common evolutionary forces could be shaping the extreme but distinct patterns of divergence in both organelle genomes within this genus.
被子植物石竹属表现出一些在细胞器基因组结构和核苷酸替代率方面最为极端和快速的分化。这些模式被认为是线粒体特异性的，因为在少数可用的核和质体基因序列中没有相关的变化。为了更好地评估线粒体和质体进化之间的关系，我们对具有完全测序线粒体基因组的四个石竹属物种的质体基因组进行了测序。我们发现，两个具有快速进化的线粒体基因组的物种，S. noctiflora 和 S. conica，其质体基因组的序列和结构进化也加速了。然而，这些变化的性质与线粒体基因组中的变化明显不同。例如，与似乎是全基因组和突变驱动的线粒体模式相反，质体替代率的加速仅限于一组基因，并优先影响非同义位点，表明在这些物种中，特定的质体编码功能受到改变的选择压力的影响。事实上，S. noctiflora 和 S. conica 中的一些质体基因显示出强烈的正选择证据。相比之下，两个具有更慢进化的线粒体基因组的物种，S. latifolia 和 S. vulgaris，其质体基因的核苷酸替代率相应较低，并且质体基因组结构自被子植物起源以来基本保持不变。这些结果提出了一种可能性，即共同的进化力量可能正在塑造该属内这两个细胞器基因组中极端但不同的分化模式。
