BACKGROUND Allium macranthum and Allium fasciculatum are two sister species and their natural populations are separated by high mountains and deep valleys with exact opposite habitat. The chloroplast genome in angiosperms has showed useful for investigating plant evolution and systematic studies. OBJECTIVE Comparative analysis of these genomes revealed potential markers and phylogenetic analysis, and discuss the influence of positive selected sites on adaptive evolution. METHODS Here, we sequenced the complete chloroplast genomes of these two species and analyzed the repeat sequences components, nucleotide diversity, selection pressure and the phylogeny relationships with related species. RESULTS A typical quadripartite structure was detected with a genome size changed from 152,148 to 152,931 bp. We identified 67 and 79 simple sequence repeats in A. macranthum and A. fasciculatum, in which the mono-nucleotide repeats A/T possess the highest percentage. Three mutational hotspots (rpl32, rps16 and matK) at the SSC and LSC regions were observed, which showed remarkably higher Pi value (> 0.03). Additionally, eight genes (rpoA, atpF, cemA, rps4, ccsA, rpoC2, rpl14 and clpP) exhibited elevated pairwise Ka/Ks ratios in alpine species. Phylogenetic analyses based on the CDS sequences and the whole complete genomes showed same topologies with high support, and A. macranthum was closely clustered with A. fasciculatum within the fourteen Amaryllidaceae species. CONCLUSION Their coding proteins of these genes often functioned in chloroplast protein synthesis, gene transcription, energy transformation and regulation and photosynthesis. These results provide valuable insights into the alpine species adaptation and evolution.

中文翻译：

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两种姐妹物种葱属Macranthum和A. fasciculatum的叶绿体基因组比较为适应性进化提供了宝贵的见识。

背景技术Macranthum葱属和fasciculatum葱属是两个姊妹物种，它们的自然种群被高山和深谷隔开，栖息地恰好相反。已显示被子植物中的叶绿体基因组可用于研究植物进化和系统研究。目的对这些基因组的比较分析揭示了潜在的标记和系统发育分析，并讨论了阳性选择位点对适应性进化的影响。方法在这里，我们对这两个物种的完整叶绿体基因组进行了测序，并分析了重复序列组成，核苷酸多样性，选择压力以及与相关物种的系统发育关系。结果检测到一个典型的四方结构，基因组大小从152,148变为152,931 bp。我们在A. Macranthum和A. fasciculatum中鉴定出67和79个简单序列重复序列，其中单核苷酸重复序列A / T的百分比最高。在SSC和LSC区域观察到三个突变热点（rpl32，rps16和matK），其Pi值显着较高（> 0.03）。此外，八个基因（rpoA，atpF，cemA，rps4，ccsA，rpoC2，rpl14和clpP）在高山物种中成对的Ka / Ks比升高。基于CDS序列和整个完整基因组的系统进化分析显示，相同的拓扑结构具有很高的支持度，并且在十四个金眼科物种中，Macranthum与A. fasciculatum紧密地聚集在一起。结论这些基因的编码蛋白通常在叶绿体蛋白合成，基因转录，能量转化和调控以及光合作用中起作用。