Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea; Nguyen Tat Thanh Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
Department of Life Science, Gachon University, Seongnam 13120, Republic of Korea.
Mol Phylogenet Evol. 2020 Jul;148:106818. doi: 10.1016/j.ympev.2020.106818. Epub 2020 Apr 12.
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.
百合目（Liliales）的单子叶植物家族表现出高度对比的光合和菌异养生活史特征。尽管之前对百合目进行了系统发育和形态学研究，但它们并未研究与这种对比现象相关的分子进化。在这里，我们使用 29 个新测序的质体基因组，对百合目所有十个科进行了首次比较质体研究，这些基因组与之前发表的数据一起进行了分析。我们还展示了 78 个质体基因和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 个基因的百合目系统发育分析。在百合目的新生成的系统发育树中，我们评估了该目选定形态特征的祖先状态变化。具有与科界限相关的不同特征的物种之间，质体基因组特征没有显着差异。然而，结果清楚地区分了百合目光合和菌异养类群在基因组结构、基因内容和顺序方面的差异。新测序的质体基因组和三基因组数据表明，Smilacaceae 是 Liliaceae 的姐妹科，而不是 Philesiaceae 和 Ripogonaceae。此外，我们提出了一个修订后的百合目科分类系统，其中包括 9 个科，将 Ripogonaceae 视为 Philesiaceae 的同义词。祖先状态重建表明，除了百合科、Melanthiaceae 和 Colchicaceae 之外，百合目的每个科都具有同源特征。还提供了一个用于所有九个百合目科的分类学关键。
