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

Abstract

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.

Keywords: Schnabelia; Chloroplast genome; Comparative genomics; Lamiaceae; Phylogenomics.

Fig. 1

Plastome maps of five Schnabelia species. The genes transcribed clockwise are shown inside of the circle while genes transcribed anti-clockwise are shown outside. The function of genes is color-coded. The dark grey color shows the GC content whereas the light grey color indicates AT content

Fig. 2

Comparison of the border positions of LSC, SSC, and IR regions in the plastomes in five Schnabelia species. JLB, LSC/IRb junction; JSB, SSC/IRb junction; JLA, LSC/IRa junction; JSA, SSC/IRa junction

Fig. 3

Repeat analysis in five plastomes of Schnabelia. (A) Frequency of repeat types. (B) Frequency of repeats by length

Fig. 4

Analysis of simple sequence repeats (SSRs) in the five Schnabelia plastomes. (A) Number of SSRs by length. (B) Distribution of SSR loci. CDS, coding DNA sequences; IGS, intergenic spacer region

Fig. 5

Heatmap of codon usage bias in five Schnabelia plastomes based on Relative Synonymous Codon Usage (RSCU) values. The color gradient (red to blue) represents normalized RSCU values, with darker red indicating stronger bias

Fig. 6

The Ka/Ks value of the 81 CDS regions in the five Schnabelia plastomes

Fig. 7

Sequence identity plots among the five Schnabelia plastomes with S. oligophylla as a reference. Annotated genes are displayed along the top. The vertical scale represents the percent identity between 50 and 100%

Fig. 8

The nucleotide variation (Pi) values of five Schnabelia plastomes were compared, with nucleotide diversity at the midpoint of the window on the x axis and within each window on the y axis (window length of 600 bp, step length of 200 bp)

Fig. 9

Phylogenetic tree of Ajugoideae based on 34 plastomes inferred using the Maximum Likelihood (ML) and Bayesian Inference (BI) method. Support values were labeled on each branch as PP (posterior probability)/BS (bootstrap support)

Fig. 10

Divergence time of Schnabelia species estimated using plastid CDS sequences. Mean divergence time (Ma) and 95% high posterior density (HPD) are shown at the branches. Arrows mark two calibration points. Node A and Node B represent the fossil constraints of subfamily Nepetoideae and genus Stachys