Department of Biology, Colorado State University, Fort Collins, CO 80523, United States.
Department of Biology, University of Virginia, Charlottesville, VA 22904, United States.
Mol Phylogenet Evol. 2014 Mar;72:82-9. doi: 10.1016/j.ympev.2013.12.004. Epub 2013 Dec 25.
In flowering plants, plastid genomes are generally conserved, exhibiting slower rates of sequence evolution than the nucleus and little or no change in structural organization. However, accelerated plastid genome evolution has occurred in scattered angiosperm lineages. For example, some species within the genus Silene have experienced a suite of recent changes to their plastid genomes, including inversions, shifts in inverted repeat boundaries, large indels, intron losses, and rapid rates of amino acid sequence evolution in a subset of protein genes, with the most extreme divergence occurring in the protease gene clpP. To investigate the relationship between the rates of sequence and structural evolution, we sequenced complete plastid genomes from three species (Silene conoidea, S. paradoxa, and Lychnis chalcedonica), representing independent lineages within the tribe Sileneae that were previously shown to have accelerated rates of clpP evolution. We found a high degree of parallel evolution. Elevated rates of amino acid substitution have occurred repeatedly in the same subset of plastid genes and have been accompanied by a recurring pattern of structural change, including cases of identical inversions and intron loss. This "syndrome" of changes was not observed in the closely related outgroup Agrostemma githago or in the more slowly evolving Silene species that were sequenced previously. Although no single mechanism has yet been identified to explain the correlated suite of changes in plastid genome sequence and structure that has occurred repeatedly in angiosperm evolution, we discuss a possible mixture of adaptive and non-adaptive forces that may be responsible.
在开花植物中，质体基因组通常是保守的，其序列进化速度比细胞核慢，结构组织变化很小或没有。然而，在分散的被子植物谱系中，质体基因组的进化速度加快了。例如，某些石竹属植物经历了一系列质体基因组的近期变化，包括倒位、反向重复边界的移动、大片段缺失、内含子丢失以及蛋白质基因亚组中氨基酸序列的快速进化，其中蛋白酶基因 clpP 的进化最为极端。为了研究序列和结构进化之间的关系，我们对三个物种（凹头勿忘草、多枝怪柳和蝇子草）的完整质体基因组进行了测序，这些物种代表了石竹族内的独立谱系，先前的研究表明它们具有加速的 clpP 进化率。我们发现了高度的平行进化。在相同的质体基因亚组中，氨基酸取代率反复升高，并伴有结构变化的重复模式，包括相同的倒位和内含子丢失。这种“综合征”的变化在密切相关的车前草或以前测序的进化较慢的石竹属物种中没有观察到。尽管尚未确定单一的机制来解释在被子植物进化中反复发生的质体基因组序列和结构的相关变化，但我们讨论了可能负责这一现象的适应性和非适应性因素的混合。
