Comparative plastome genomics and phylogenetic analyses of Liliaceae
Comparative plastome genomics and phylogenetic analyses of Liliaceae
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DOI：
10.1093/botlinnean/boaa109
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发表时间：
2021-02-10
影响因子：
2.4
通讯作者：
Fu, Cheng-Xin
中科院分区：
文献类型：
--
作者：
Lu, Rui-Sen;Yang, Tuo;Fu, Cheng-Xin
百合科主要分布在北半球温带地区，在园艺、烹饪和医药领域具有重要意义，但它也是一个长期存在分类学不确定性的科。由于所使用的分子标记有限且变异性不足，准确的物种鉴定仍面临挑战，该科各属之间的系统发育关系也依旧未得到解决和（或）缺乏有力支持。在此，对百合科9个属新测序的9个质体基因组与此前已发表的该科质体基因组数据相结合，总共提供了涵盖目前公认的全部15个属的86条完整质体基因组序列用于分析。所有这些质体基因组（146.9 - 158.3千碱基对）都具有典型的四分体结构，基因组排列和内容保守。系统发育基因组学分析有力地证实了对4个亚科的划分：包含4个属的油点草亚科；包含2个属的舞鹤草亚科；包含8个属的百合亚科；以及仅包含仙灯属的仙灯亚科，仙灯亚科与舞鹤草亚科和百合亚科互为姊妹群。在该科中鉴定出至少10个可能作为通用标记的基因间隔区，在更精细的层面上，百合属和贝母属分别有9个和7个基因间隔区具有特别高的变异性。基因间隔区rpoB - trnC、trnS - trnG、trnT - psbD和trnT - trnL显示出较高的系统发育有效性，可能是未来系统发育、种系地理学和群体遗传学研究的最佳选择。
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.