Liliaceae, distributed mainly across the temperate Northern Hemisphere, are of great horticultural, culinary and medical importance, but are also a family with a long history of taxonomic uncertainty. Challenges in accurate species identification persist and phylogenetic relationships among genera in the family continue to be unresolved and/or weakly supported due to the use of limited molecular markers with insufficient variability. Here, nine newly sequenced plastomes for nine Liliaceae genera have been combined with previously published plastome data for this family, providing a total of 86 complete plastid genome sequences covering all 15 currently recognized genera for analyses. All these plastid genomes (146.9–158.3 kb) possess the typical quadripartite structure with conserved genome arrangement and content. Phylogenomic analyses strongly confirm the recognition of four subfamilies: Tricyrtidoideae with four genera; Medeoloideae with two genera; Lilioideae with eight genera and Calochortoideae, for Calochortus alone, as sister to Medeoloideae and Lilioideae. At least ten intergenic spacer regions that may serve as universal markers were identified in the family and, on a finer scale, nine and seven intergenic spacer regions are especially variable in Lilium and Fritillaria, respectively. The intergenic spacer regions rpoB-trnC, trnS-trnG, trnT-psbD and trnT-trnL, which showed high phylogenetic effectiveness, may be the best choices for future phylogenetic, phylogeographic and population genetic studies.

中文翻译：

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百合科的比较组基因组学和系统发育分析

百合科主要分布在温带的北半球，在园艺，烹饪和医学上具有重要意义，但也是一个有着悠久的分类学不确定性历史的家庭。由于使用有限的变异性不足的分子标记，在准确的物种识别中仍然存在挑战，并且该家族属之间的系统发育关系仍未得到解决和/或支持较弱。在这里，已经将9个百合科的9个新测序的质体组与该家族先前发布的质体组数据相结合，提供了总共86个完整的质体基因组序列，涵盖了目前分析的15个属。所有这些质体基因组（146.9–158.3 kb）均具有典型的四方结构，且基因组排列和内容均得到保守。系统发育学分析强有力地证实了对四个亚科的识别：具有四个属的三角亚纲；甲虫科有两个属；八属的百合科和鳞翅目科独生一头Calochortus，作为Medeoloideae和Lilioideae的姐妹。在该家族中鉴定出至少十个可用作通用标记的基因间隔区，并且在更精细的规模上，百合属和贝母中的九个和七个基因间隔区分别是可变的。基因间隔区rpoB - trnC，trnS - trnG，trnT - psbD和trnT - trnL表现出很高的系统发育效果，可能是未来系统发育，系统学和种群遗传学研究的最佳选择。