In the most recent classification of Rutaceae, Amyridoideae is the largest and most diverse subfamily. In Amyridoideae, the genera Phellodendron, Tetradium, Toddalia and Zanthoxylum were proposed as “proto-Rutaceae”due to substantial phytochemical similarities. In this study, we investigated the plastome varia-tions in eight species representing these four genera and Melicope. All plastomes exhibited a typical quadripartite structure with four regions (LSC, SSC, IRa and IRb). The whole chloroplast genome size ranged from 158,383 bp to 159,014 bp and the gene number ranged from 115 to 116. By comparative analyses, we found that there were structural variations at the LSC/IR and SSC/IR borders of the plastomes in the five genera, especially in Melicope. Three most divergent regions (trnH-psbA, trnE-trnT and psaB) were found from the LSC region, which had great potential for developing effective genetic markers. In addition, we conducted a phylogenomic analyses of the “proto-Rutaceae”and related taxa with plastomes data from 36 species. Our results showed that (1) Phellodendron, Tetradium, Toddalia and Zanthoxylum were confirmed as close relatives and grouped together as the ‘proto-Rutaceae’, (2) Phellodendron was sister to Tetradium, and Toddalia was deeply nested within Zanthoxylum, and (3) Toddalia asiatica was closely related to the Southwest Pacific and East Asian species of Zanthoxylum, and Melicope pteleifolia was more closely related to Acronychia than it is to Tetradium. This study provided new insights into the plastome structural varia-tions in subfamily Amyridoideae, and demonstrated that the plastomes data were sufficiently robust to explore implications of the phylogeny for the previous phylogenetic hypotheses.

中文翻译：

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Amyridoideae（Rutaceae）亚科五个属的质粒的比较分析和系统发育意义

在芸香科的最新分类中，Amyridoideae是最大和最多样化的亚科。在Amyridoideae中，属黄柏，吴茱萸属，飞龙掌血和花椒由于存在大量的植物化学相似性，因此被提议为“原芸香科”。在这项研究中，我们调查了代表这四个属和Melicope的八个物种的质体变化。所有质体均显示具有四个区域（LSC，SSC，IRa和IRb）的典型四方结构。整个叶绿体基因组大小范围为158,383 bp至159,014 bp，基因编号范围为115至116。通过比较分析，我们发现五个属的质体的LSC / IR和SSC / IR边界存在结构变异。尤其是在Melicope中。三个差异最大的区域（trnH-psbA，trnE-trnT和psaB）是在LSC地区发现的，具有开发有效遗传标记的巨大潜力。此外，我们使用来自36个物种的质体组数据对“原始芸香科”和相关的类群进行了植物学分析。我们的结果表明：（1）黄柏，吴茱萸属，飞龙掌血以及花椒被证实为近亲和分组在一起作为“原芸香科”，（2）黄柏是姐妹吴茱萸属，和飞龙掌血被深深嵌套在花椒，和（3 ）Toddalia asiatica与西南太平洋和东亚花椒属密切相关，并且Melicope pteleifolia与Acronychia的关系比与Tetradium的关系更为紧密。这项研究提供了新的见解，亚纲蝇亚科的塑性组结构变异，并证明了塑性组数据足够强大，以探讨系统发育对以前的系统发育假说的影响。