BACKGROUND AND AIMS The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. METHODS In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. RESULTS Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. CONCLUSIONS Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.

中文翻译：

---

基于全质体序列洞察葱属（石蒜科）的系统发育、年龄和进化

背景和目的 葱属是最大的单子叶属之一，包括许多具有营养和药用价值的经济上重要的作物，几个世纪以来一直是分类或系统发育研究的焦点。 . ． ．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．．最近的研究表明该属可分为15个亚属和72个部分，进一步分为三个进化谱系。然而，由一两个位点重建的系统发育关系显示出较弱的支持，尤其是对于第三个进化谱系，可能无法非常清楚地显示物种关系，并可能阻碍进一步的适应性和进化研究。方法本研究共收集了39个葱属完整叶绿体基因组（涵盖12个葱属亚属），并将这些与来自其他 19 个单子叶植物科的 125 种塑性体相结合，我们重建了葱属的系统发育，估计了三个进化谱系的起源和发散时间，并研究了该属及其相关科的适应性进化。结果我们的系统发育分析证实了葱属的单系和三个进化谱系，而在第三个进化谱系中检测到新的物种关系。三个进化谱系的分歧时间估计在始新世早期到中新世中期，并且在葱属物种中发现了许多阳性选择基因（PSGs）和具有高平均Ka/Ks值的PSGs。结论我们的结果检测到了葱属植物的系统发育关系。具有高 Ka/Ks 值的 PSG 和 PSG，以及多样化的形态、复杂的染色体特征和独特的繁殖方式可能在葱属物种的适应和进化中发挥重要作用。这是第一项结合塑性体、形态学和细胞学数据对葱属进行系统发育和进化分析的研究。我们希望这项研究可以为其他研究人员进一步分析葱属植物做出贡献。