Wei Shengnan, Ying Jianan, Lu Mengxia, Li Jie, Huang Yanbo, Wu Zhenming, Nevill Paul, Li Pan, Jin Xinjie, Lu Qixiang
Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
Jiashan Lige Ecological Technology Co. Ltd, Jiashan, 314113, China.
BMC Plant Biol. 2025 May 7;25(1):600. doi: 10.1186/s12870-025-06647-y.
Schnabelia species, herbaceous perennial plants within the Lamiaceae family, possess medicinal value and are endemic to China. While previous studies have focused on morphological classification, molecular systematics, and medicinal components, there has been limited research on phylogenomics. To reveal their plastid genome characteristics and phylogenetic relationships, we sequenced and assembled the plastomes of all five Schnabelia species (S. oligophylla, S. tetrodonta, S. nepetifolia, S. terniflora, S. aureoglandulosa), conducted comparative genomic analyses, and constructed a phylogenetic tree incorporating closely related taxa in subfamily Ajugoideae, as well as conducting divergence time estimation.
Plastome size of the five species ranged from 155,733 bp to 156,944 bp, encompassing 115 unique genes, with a GC content of 37.8% same for all species. Five intergenic spacer regions (trnH-GUG-psbA, trnK-UUU-matK, petB-petD, ndhD-psaC, ndhA-ndhH) were identified as divergence hotspots. Gene selection pressure analysis demonstrated that all genes were under negative selection. Phylogenetic relationship of Ajugoideae species based on plastomes confirmed the monophyly of Schnabelia. Two clades within Schnabelia were supported, one containing two original species and the other comprising three species transferred from Caryopteris. The stem age of the Schnabelia is estimated to be approximately 30.24 Ma, with the split of two Sections occurring around 12.60 Ma.
We revealed plastid genome evolutionary features for five species within the genus Schnabelia. The identified highly variable regions can provide a tool for future identification of these medicinal plants. The diversification of Schnabelia during middle Miocene and the Quaternary suggests that historical geological and climatic shifts facilitated species differentiation. These findings enhance our understanding of Schnabelia's evolution and support future research on chloroplast diversity, aiding conservation and sustainable use.
黄芩属植物为唇形科多年生草本植物，具有药用价值，是中国特有的植物。虽然之前的研究集中在形态分类、分子系统学和药用成分上，但关于系统发育基因组学的研究却很少。为了揭示它们的质体基因组特征和系统发育关系，我们对黄芩属的所有五个物种（少花黄芩、四齿黄芩、尼泊尔黄芩、三花黄芩、金黄腺毛黄芩）的质体基因组进行了测序和组装，进行了比较基因组分析，并构建了一个包含筋骨草亚科近缘类群的系统发育树，同时进行了分歧时间估计。
这五个物种的质体基因组大小在155,733 bp至156,944 bp之间，包含115个独特基因，所有物种的GC含量均为37.8%。五个基因间隔区（trnH-GUG-psbA、trnK-UUU-matK、petB-petD、ndhD-psaC、ndhA-ndhH）被确定为分歧热点。基因选择压力分析表明所有基因都受到负选择。基于质体基因组的筋骨草亚科物种系统发育关系证实了黄芩属的单系性。支持黄芩属内的两个分支，一个包含两个原始物种，另一个包含从莸属转移过来的三个物种。黄芩属的起源时间估计约为3024万年前，两个组的分化发生在约1260万年前。
我们揭示了黄芩属五个物种的质体基因组进化特征。所确定的高度可变区域可为未来这些药用植物的鉴定提供工具。黄芩属在中新世中期和第四纪的多样化表明，历史地质和气候变化促进了物种分化。这些发现增进了我们对黄芩属进化的理解，并支持未来对叶绿体多样性的研究，有助于保护和可持续利用。
