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. 2026 Sep 29;11(10):1251–1255. doi: 10.1080/23802359.2026.2739024

The complete chloroplast genome of Lamium purpureum L. var. purpureum (Lamiaceae) and phylogenetic analysis

Young-Kee Kim a, Yu-jin Jeon b, Jun-Ho Song a,b,✉
PMCID: PMC13629799  PMID: 42824913

Abstract

Lamium purpureum var. purpureum, the autonym of L. purpureum, is one of five infraspecific taxa currently recognized within the species. In this study, we report the complete chloroplast genome of Lamium purpureum var. purpureum (150,474 bp) with a typical quadripartite structure. A total of 116 unique genes were annotated, comprising 79 protein-coding genes, 33 transfer RNA genes, and four ribosomal RNA genes. Phylogenetic analysis recovered the subfamily Lamioideae and the genus Lamium as monophyletic with strong bootstrap support (100%). Within Lamium, L. purpureum var. purpureum was resolved as closely related to L. purpureum (PP203137).

Keywords: Lamium purpureum var. purpureum, Lamiaceae, chloroplast genome, phylogeny

Introduction

Lamium L. 1753 (Lamioideae Harley, Lamiaceae Martinov = Labiatae) comprises approximately 16–40 species distributed in the temperate and subtropical regions of Asia, North Africa, and Europe (Mennema 1989; Harley et al. 2004; Bendiksby et al. 2011; Salehi et al. 2019).

Lamium purpureum L. 1753 is the type species of the genus Lamium (Britton and Brown 1913; Mennema 1989). Historically, the infraspecific taxa of L. purpureum comprised five members (Mennema 1989; Govaerts et al. 2021). Lamium purpureum is a wild edible plant traditionally used for medicinal purposes and investigated for several biological activities (Akkol et al. 2008; Bubueanu et al. 2019).

The chloroplast genomes exhibit a highly conserved circular quadripartite structure, comprising a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs) (Palmer 1991). Specific loci within these genomes have been extensively used as DNA barcodes for precise species identification and broad phylogenetic inference (CBOL Plant Working Group 2009).

With advancements in sequencing technologies, an increasing number of chloroplast genomes have been published in recent years. In this study, we assembled the complete chloroplast genome of L. purpureum var. purpureum and investigated molecular phylogenetic relationships within Lamium species. The chloroplast genome data generated in this study provide a valuable resource for advancing species identification, conservation strategies, and evolutionary research.

Materials and methods

In this study, fresh leaf material of L. purpureum var. purpureum was collected from Gunsan-si, Jeollabuk-do, Republic of Korea (35°48′11.4ʺN 126°25′22.5ʺE, Figure 1). A voucher specimen was deposited in the Herbarium of Chungbuk National University (Herbarium Code: CBU; J.-H. Song, jhsong@chungbuk.ac.kr) under the collection and voucher accession numbers CBU-C-163 and CBU-V-89, respectively. The dried leaves were ground into a fine powder in liquid nitrogen using a mortar and pestle. Total genomic DNA was extracted from the powdered tissue using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. DNA quality and integrity were evaluated by agarose gel electrophoresis and 4200 TapeStation (Agilent, Santa Clara, CA).

Figure 1.

Three plant images: A shows a dense cluster of purple flowers and green foliage. B presents a close-up of a flowering plant with green and purple leaves. C is a herbarium specimen illustrating the plant's structure and roots against a white background.

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Photographs of Lamium purpureum var. purpureum. (A) Habit. (B) An individual in its natural habitat. Herbs, annual, or biennial. Leaves orbicular to reniform. Floral leaves short petiolate, often purplish, triangular-ovate. Corolla tube straight without hairy annulus inside. (C) Collected voucher specimen. Photographs of L. purpureum var. purpureum were taken on Munyeodo Island, Okdo-myeon, Gunsan-si, Jeollabuk-do, South Korea (35°48′11.3ʺN 126°25′22.4ʺE) by Yu-jin Jeon (the second author).

Total genomic DNA was sent to Macrogen (Seoul, South Korea) for library preparation and 151-bp paired-end short-read sequencing on the Illumina NovaSeq (Illumina, San Diego, CA), yielding 39,813,483 read pairs (12.0 Gb of raw data), of which 11.3 Gb (94.5%) had a base quality of ≥ Q30. Adapter removal and quality filtering were performed using Trimmomatic v.0.39 (Bolger et al. 2014) with the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The resulting reads were used for de novo assembly of the chloroplast genome using NOVOPlasty v.4.3.1 (Dierckxsens et al. 2017) with a k-mer size of 33 and four protein-coding genes (matK, rbcL, ndhH, and ycf2) from L. takeshimense (MN240520) as the seed sequences. To estimate sequencing coverage depth, the assembled chloroplast genome and the trimmed reads were aligned using BWA (Li 2013) and per-base coverage depth was calculated using SAMtools v1.21 (Danecek et al. 2021). Genome annotation was conducted in Geneious R10.2.6 using Lamium takeshimense Nakai (MN240520) as the reference. The circular chloroplast genome map was visualized using OGDraw (Greiner et al. 2019), and the schematic representation of cis- and trans-spliced genes was generated using CPGView (Liu et al. 2023).

The phylogenetic position of L. purpureum var. purpureum was inferred using 38 complete chloroplast genomes, comprising the newly sequenced L. purpureum var. purpureum together with 35 additional representative taxa from the family Lamiaceae (36 taxa spanning 12 subfamilies) and two outgroup taxa. All chloroplast genome sequences except that of the target species (L. purpureum var. purpureum) were retrieved from GenBank (NCBI). A total of 79 protein-coding genes and four ribosomal RNA (rRNA) genes were extracted from each of the chloroplast genomes. Sequence alignments were performed using MAFFT v.7.475 (Katoh et al. 2002) with default parameters. Poorly aligned regions were removed using trimAl v.1.2 (Capella-Gutiérrez et al. 2009). The trimmed alignments were concatenated using AMAS (Borowiec 2016). For each alignment, the best-fit nucleotide substitution model was determined using ModelFinder (Kalyaanamoorthy et al. 2017) and the best-fit substitution models are listed in Table S1. A maximum-likelihood (ML) phylogenetic tree was constructed based on the concatenated dataset with a partitioned nucleotide substitution model scheme using IQ-TREE2 (Minh et al. 2020), with 1000 ultrafast bootstrap replicates (Hoang et al. 2018). The final phylogenetic tree was visualized using TreeGraph2 (Stöver and Müller 2010).

Results

The complete chloroplast genome of L. purpureum var. purpureum is 150,474 bp in length, with an overall GC content of 38.6% and a mean sequencing coverage depth of 3896.4× (minimum: 1497×, maximum: 7800×; Figure S1). The chloroplast genome exhibits the typical quadripartite structure characteristic of most angiosperms, consisting of an LSC region (82,458 bp) and an SSC region (17,004 bp), separated by two IR regions (25,506 bp each) (Figure 2).

Figure 2.

Circular diagram of Lamium purpureum chloroplast genome (150,474 bp) with labeled genes, regions (LSC, SSC, IRA), and color-coded categories. The figure presents a circular representation of the chloroplast genome of Lamium purpureum var. purpureum, totaling 150,474 base pairs. It features two rings: the outer ring displays color-coded gene annotations and genomic regions—Large Single Copy (LSC), Small Single Copy (SSC), and inverted repeat regions (IRa and IRb). 14 categories, including photosystems, ATP synthase, and ribosomal proteins, are color-coded for easy identification. The inner ring represents GC content, with the light-gray region indicating overall nucleotide content. Each label indicates the corresponding gene’s placement, offering a detailed overview of the genome's structure.

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Chloroplast genome map of Lamium purpureum var. purpureum. Genes located on the inner side of the circular map are transcribed in the clockwise direction, while those on the outer side are transcribed counterclockwise. The innermost dark gray part represents the GC content, with the light gray indicating overall nucleotide content. Genes are color-coded according to their functional categories. The thick line on the outer circle indicates the boundaries of the inverted repeat regions (IRa and IRb), which partition the genome into the large single-copy (LSC) and small single-copy (SSC) regions.

A total of 116 unique genes were annotated, comprising 79 protein-coding genes, 33 transfer RNA (tRNA) genes, and four rRNA genes, with no evidence of gene loss or pseudogenization. Among the protein-coding genes, 12 contained one or two introns. Eleven genes (atpF, clpP, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, rps16, and ycf3) were identified as cis-spliced genes (Figure S2), while one gene (rps12) was identified as a trans-spliced gene (Figure S3).

When compared with other reported Lamium chloroplast genomes, no significant inversions, large-scale rearrangements, expansions, or contractions of the IR regions, or gene losses were observed (Figure S4). Based on the consensus sequence derived from the MAFFT alignment (visualized in Geneious R10.2.6), five intergenic spacer (IGS) regions, ndhC–trnV-UAC, matK-rps16, rpl32-trnL-UAG, trnS-GGA-rps4, and trnT-GGU–psbD, appeared more variable than other Lamium species. Phylogenetic analysis based on 36 Lamiaceae species and two outgroup taxa provided strong support for the monophyly of the subfamily Lamioideae (Figure 3). Furthermore, L. purpureum var. purpureum was found to be sister to L. purpureum (PP203137).

Figure 3.

Phylogenetic tree displaying relationships among over 30 plant species in the Lamiaceae family, highlighting Lamium purpureum var. purpureum (PZ055112) in red. The figure shows a phylogenetic tree representing evolutionary relationships among over 30 plant species, primarily from the Lamiaceae family. The horizontal tree has Lamium purpureum var. purpureum PZ055112 highlighted in red. It includes bootstrapped support values at various nodes (e.g., 64, 87, 99) and vertical brackets indicating major taxonomic groups like Lamioideae and Scutellarioideae. The branches illustrate genetic distances, with related families like Verbenaceae and Mazaceae positioned at the bottom, showcasing their relationships with Lamiaceae species.

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Maximum-likelihood phylogenetic tree inferred from the concatenated matrix (80,170 bp) of 79 protein-coding and four rRNA genes using IQ-TREE2. Lamium purpureum var. purpureum (PZ055112) was highlighted in bold and red color. The following sequences were used: Agastache rugosa (NC053706), Ajuga bracteosa (NC068635), Ballota nigra (NC066022), Betonica officinalis (NC085507), Callicarpa americana (NC052696), Chelonopsis souliei (NC058326), Clerodendrum bungei (NC056141), Coleus hadiensis (NC069583), Colquhounia coccinea (NC058329), Congea tomentosa (NC058332), Cymaria dichotoma (NC058333), Dicrastylis parvifolia (NC058335), Elsholtzia byeonsanensis (NC064501), Garrettia siamensis (MT473760), Galeopsis bifida (NC071846), Glandularia tenera (NC057678), Gmelina hainanensis (NC053620), Lagopsis supina (NC058246), Lamium album (NC036971), Lamium barbatum (PV802395), Lamium takeshimense (MN240520), Lamium galeobdolon (NC036972), Lamium amplexicaule (MT473770), Lamium purpureum (PP203137), Leonotis leonurus (PP093763), Macbridea alba (MT473771), Mazus humilis (NC077631), Paraphlomis foliata (NC085509), Phlomoides eriocalyx (NC085446), Pogostemon cablin (NC042796), Prostanthera campbellii (NC084414), Rotheca myricoides (NC059906), Schnabelia nepetifolia (NC088035), Scutellaria amoena (NC057255), Stachys chamissonis (NC029822), Tectona grandis (NC020098), and Vitex bicolor (NC065871). A total of 36 representative taxa from the family Lamiaceae and two outgroup taxa (Glandularia tenera for the Verbenaceae and Mazus humilis for the Mazaceae) were used to construct the phylogenetic tree. Bootstrap support values from 1000 replicates are shown at each node; an asterisk above or below a node indicates a bootstrap value of 100%. The scale bar represents 0.02 substitutions per site.

Discussion and conclusions

The genome size, gene content, and gene order were highly conserved (mean pairwise identity 97.1%), suggesting that the overall architecture of the chloroplast genome has remained stable throughout the diversification of the genus. This high degree of conservation aligns with the general pattern observed in other genera within the family Lamiaceae, where chloroplast genome structure is typically well-preserved across closely related taxa (Zhao et al. 2021). The cis-/trans-spliced configuration observed here—11 cis-spliced genes and the trans-spliced rps12—is consistent with that reported across angiosperm plastomes.

An ML phylogenetic tree was constructed to infer the phylogenetic relationships of L. purpureum var. purpureum within the family Lamiaceae (Figure 3). The subfamily Lamioideae was recovered as monophyletic with strong bootstrap support (100%). Within the subfamily Lamioideae, the genus Lamium also forms a monophyletic clade consistent with previous findings (Park et al. 2019; Du et al. 2025). The phylogenetic tree confirmed that the genus Lamium is closely related to the genus Leonotis (Pers.) R.Br., consistent with previous findings (Zhao et al. 2021). As the chloroplast genome is maternally inherited in most angiosperms, the phylogeny presented here reflects the maternal lineage of L. purpureum var. purpureum rather than its complete evolutionary history. Although the plastome phylogeny suggested close affinities among the two L. purpureum accessions, L. amplexicaule, and L. galeobdolon, resolving their relationships will require evidence from nuclear markers and more comprehensive taxon sampling.

In conclusion, this study reports the complete chloroplast genome of L. purpureum var. purpureum and provides a genomic resource for future taxonomic and phylogenetic studies of Lamium.

Supplementary Material

Table_S1_Models.csv
TMDN_A_2739024_SM7057.csv (1.3KB, csv)

Acknowledgments

We thank the members of the Laboratory of Plant Systematics (LPS), Chungbuk National University (CBNU), for their valuable assistance and support throughout this study. We also sincerely thank the editor and the three anonymous reviewers for their constructive comments and valuable suggestions that improved this manuscript.

Funding Statement

This research was supported by Global – Learning & Academic Research Institution for Master’s/PhD Students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education (Grant number: RS-2024-00445180) and the Korea Forest Service (Korea Forest Research Institute) under the Forestry Science and Technology Development Project (Project Number: RS-2021-KF001796).

Ethical approval

The plant material used in this study was not obtained from an endangered or protected species. The sampling site was not located within a protected area, and collection of the plant material did not require specific permission from the relevant authorities. The voucher specimen was identified by Jun-Ho Song (correspondence, jhsong@chungbuk.ac.kr) and deposited at CBU under voucher numbers CBU-C-163 and CBU-V-89.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI under the accession number (PZ055112). The associated SRA, BioProject, and BioSample numbers are SRX32357368, PRJNA1429014, and SAMN55977550, respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Table_S1_Models.csv
TMDN_A_2739024_SM7057.csv (1.3KB, csv)

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI under the accession number (PZ055112). The associated SRA, BioProject, and BioSample numbers are SRX32357368, PRJNA1429014, and SAMN55977550, respectively.

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