The families of the monocot order Liliales exhibit highly contrasting characteristic of photosynthetic and mycoheterotrophic life histories. Although previous phylogenetic and morphological studies of Liliales have been conducted, they have not examined molecular evolution associated with this contrasting phenomenon. Here, we conduct the first comparative plastome study of all ten families of Liliales using 29 newly sequenced plastid genomes analyzed together with previously published data. We also present a phylogenetic analysis for Liliales of 78 plastid genes combined with 22 genes from all three genomes (nuclear 18S rDNA and phyC; 17 plastid genes; and mitochondrial matR, atpA, and cob). Within the newly generated phylogenetic tree of Liliales, we evaluate the ancestral state changes of selected morphological traits in the order. There are no significant differences in plastid genome features among species that show divergent characteristics correlated with family circumscriptions. However, the results clearly differentiate between photosynthetic and mycoheterotrophic taxa of Liliales in terms of genome structure, and gene content and order. The newly sequenced plastid genomes and combined three-genome data revealed Smilacaceae as sister to Liliaceae instead of Philesiaceae and Ripogonaceae. Additionally, we propose a revised familial classification system of Liliales that consists of nine families, considering Ripogonaceae a synonym of Philesiaceae. The ancestral state reconstruction indicated synapomorphies for each family of Liliales, except Liliaceae, Melanthiaceae and Colchicaceae. A taxonomic key for all nine families of Liliales is also provided.

中文翻译：

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真百合（单子叶植物顺序莉莉亚莱斯）中质体组进化的意义。

单子叶植物顺序百合科的家庭表现出光合和真菌异养生活史的高度对比特征。尽管以前已经对Liliales进行了系统发育和形态学研究，但他们尚未检查与此相反现象相关的分子进化。在这里，我们使用分析的29个新测序的质体基因组以及以前发表的数据，对Liliales的所有10个家族进行了首次比较性质体研究。我们还提出了系统发育分析，分析了78个质体基因与来自所有三个基因组（核18S rDNA和phyC； 17个质体基因；以及线粒体matR，atpA和cob）的22个基因相结合的系统发育分析。在新近生成的Liliales系统树中，我们按顺序评估了选定形态特征的祖先状态变化。在物种之间的质体基因组特征上没有显着差异，这些物种显示与家族限制相关的不同特征。然而，从基因组结构，基因含量和顺序上看，结果清楚地区分了莉利亚斯的光合和异养菌类群。新测序的质体基因组和结合的三基因组数据显示，S科是百合科的姊妹科，而不是费城科和Ripogonaceae。此外，我们提出了修订的Liliales家族分类系统，该系统由9个科组成，认为Ripogonaceae是Philesiaceae的同义词。祖先状态的重建表明除了百合科，伞形科和菊科以外，每个百合科的亚同型。还提供了Liliales的所有9个家庭的分类密钥。