Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest number of species. Morphological characters such as fruit anatomy, leaf morphology and subterranean structures of Angelica species show extreme diversity. Consequently, the taxonomic classification of Angelica species is complex and remains controversial, as the classifications proposed by previous studies based on morphological data and molecular data are highly discordant. In addition, the phylogenetic relationships of major clades in the Angelica group, particularly in the Angelica s. s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used in phylogenetic studies and for evaluating genetic diversity. In this study, we sequenced and assembled 28 complete cp genomes from 22 species, two varieties and two cultivars of Angelica. Combined with 36 available cp genomes in GenBank from representative clades of the subfamily Apioideae, the characteristics and evolutionary patterns of Angelica cp genomes were studied, and the phylogenetic relationships of Angelica species were resolved. The Angelica cp genomes had the typical quadripartite structure including a pair of inverted repeats (IRs: 5836–34,706 bp) separated by a large single-copy region (LSC: 76,657–103,161 bp) and a small single-copy region (SSC: 17,433–21,794 bp). Extensive expansion and contraction of the IR region were observed among cp genomes of Angelica species, and the pattern of the diversification of cp genomes showed high consistency with the phylogenetic placement of Angelica species. Species of Angelica were grouped into two major clades, with most species grouped in the Angelica group and A. omeiensis and A. sinensis grouped in the Sinodielsia with Ligusticum tenuissimum. Our results further demonstrate the power of plastid phylogenomics in enhancing the phylogenetic reconstructions of complex genera and provide new insights into plastome evolution across Angelica L.

中文翻译：

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当归塑性体反向重复序列的系统发育和进化动力学

当归 L.（伞形科）是经济上重要的属，包括约。一百十种。当归物种在北半球的所有大陆都有发现，东亚拥有最多的物种。当归物种的果实解剖结构、叶片形态和地下结构等形态特征表现出极大的多样性。因此，当归物种的分类学分类是复杂的并且仍然存在争议，因为先前基于形态学数据和分子数据的研究提出的分类高度不一致。此外，当归组中主要进化枝的系统发育关系，尤其是当归 ss 进化枝，仍不清楚。叶绿体 (cp) 基因组序列已广泛用于系统发育研究和评估遗传多样性。在这项研究中，我们对来自当归的 22 个物种、两个变种和两个栽培品种的 28 个完整 cp 基因组进行了测序和组装。结合GenBank中来自Apiideae亚科代表性进化枝的36个可用cp基因组，研究了当归cp基因组的特征和进化模式，解析了当归物种的系统发育关系。当归 cp 基因组具有典型的四分体结构，包括一对反向重复序列（IR：5836-34,706 bp），由一个大的单拷贝区域（LSC：76,657-103,161 bp）和一个小的单拷贝区域（SSC：17,433 –21,794 bp）。在当归物种的 cp 基因组中观察到 IR 区域的广泛扩张和收缩，cp基因组的多样化模式与当归物种的系统发育位置高度一致。当归的种类被分为两个主要的进化枝，大多数物种被归入当归组，而峨眉曲霉和中华白芷与当归一​​起归入华夏草。我们的结果进一步证明了质体系统基因组学在增强复杂属的系统发育重建方面的力量，并为当归的质体进化提供了新的见解。