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Background <p><i>Schnabelia</i> 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 <i>Schnabelia</i> species (<i>S. oligophylla</i>, <i>S. tetrodonta</i>, <i>S. nepetifolia</i>, <i>S. terniflora</i>, <i>S. aureoglandulosa</i>), conducted comparative genomic analyses, and constructed a phylogenetic tree incorporating closely related taxa in subfamily Ajugoideae, as well as conducting divergence time estimation.</p> Results <p>Plastome size of the five species ranged from 155,733&#xa0;bp to 156,944&#xa0;bp, encompassing 115 unique genes, with a GC content of 37.8% same for all species. Five intergenic spacer regions (<i>trn</i>H<i>-GUG-psb</i>A, <i>trn</i>K<i>-UUU-mat</i>K, <i>pet</i>B<i>-pet</i>D, <i>ndh</i>D<i>-psa</i>C, <i>ndh</i>A<i>-ndh</i>H) 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 <i>Schnabelia</i>. Two clades within <i>Schnabelia</i> were supported, one containing two original species and the other comprising three species transferred from <i>Caryopteris</i>. The stem age of the <i>Schnabelia</i> is estimated to be approximately 30.24&#xa0;Ma, with the split of two Sections occurring around 12.60&#xa0;Ma.</p> Conclusions <p>We revealed plastid genome evolutionary features for five species within the genus <i>Schnabelia</i>. The identified highly variable regions can provide a tool for future identification of these medicinal plants. The diversification of <i>Schnabelia</i> during middle Miocene and the Quaternary suggests that historical geological and climatic shifts facilitated species differentiation. These findings enhance our understanding of <i>Schnabelia</i>’s evolution and support future research on chloroplast diversity, aiding conservation and sustainable use.</p>

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Plastome comparison and phylogenomics of Chinese endemic Schnabelia (Lamiaceae): insights into plastome evolution and species divergence

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年5月7日

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  • Shengnan Wei,
  • Jianan Ying,
  • Mengxia Lu,
  • Jie Li,
  • Yanbo Huang,
  • Zhenming Wu,
  • Paul Nevill,
  • Pan Li,
  • Xinjie Jin,
  • Qixiang Lu

摘要

Background

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.

Results

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.

Conclusions

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.