Do Hoang Dang Khoa, Kim Joo-Hwan
Plant Systematics Laboratory, Department of Biological Science, Gachon UniversitySeongnam, South Korea.
Front Plant Sci. 2017 May 22;8:693. doi: 10.3389/fpls.2017.00693. eCollection 2017.
Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species (Korea) and (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the region across the Melanthiaceae. Based on the partial or complete loss of gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections ( and ) of . Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from to a part of . Our results show an accumulation of tandem repeats in the regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.
叶绿体基因组（cpDNA）是被子植物进化研究中极具价值的资源，因为它们高度保守、体积小且在植物中发挥着关键作用。滑链错配（SSM）被认为是在cpDNA中产生重复单元的一种机制。然而，关于通过SSM事件使用不同小重复序列的研究尚未见报道，而这种事件可能会在cpDNA的同一区域内诱导不同类型重复序列的积累。在这里，我们对来自韩国特有物种和美国特有物种的两个叶绿体基因组进行了测序，以填补分子数据之间的空白，并探索藜芦科基因组事件的“热点”。对23个完整cpDNA序列的比较分析表明，藜芦科不同物种的 区域存在不同阶段的缺失。基于cpDNA中 基因的部分或完全缺失，我们首次报道了可用于识别藜芦科两个组（ 和 ）的潜在分子标记。藜芦科在大单拷贝和反向重复区域之间的连接处表现出显著变化，范围从 到 的一部分。我们的结果表明cpDNA的 区域存在串联重复序列的积累。在对百合目大多数被研究类群的该区域进行进一步观察时发现，存在小的保守序列且位于串联重复序列两侧。因此，我们提出了三种情况，即在SSM事件期间使用不同的小重复序列来产生新的不同类型的重复序列。偶尔，在SSM过程之前，会发生点突变事件和双链断裂修复，并诱导形成SSM过程中不可或缺的初始重复单元。在藜芦族（藜芦科，百合目）中，短重复序列的SSM可能比长重复序列更频繁发生。总的来说，这些发现为叶绿体基因组中SSM的动态结果增添了新证据，这可能有助于被子植物的进一步进化研究。此外，cpDNA中的基因组事件是百合目挖掘分子标记的潜在资源。
