In Silico Phylogenetic Analysis of Lamiaceae Based on ITS, matK, and rbcL DNA Barcodes

Chayra Endlessa; Topik Hidayat; Siti Sriyati

doi:10.5614/3bio.2026.8.1.4

In Silico Phylogenetic Analysis of Lamiaceae Based on ITS, matK, and rbcL DNA Barcodes

Published: 2026-01-01 | DOI: 10.5614/3bio.2026.8.1.4 | Vol 8, Issue 1 (2026)

Authors

Chayra Endlessa

OpenAlex: A5123337212

Topik Hidayat

OpenAlex: A5033818550

Siti Sriyati

OpenAlex: A5123303933

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Abstract

Lamiaceae, widely used as herbal medicine, is increasingly vulnerable to adulteration driven by market demand, compromising product safety and efficacy. Prevention is challenging due to morphological similarities; thus, DNA-based phylogenetics offer an alternative for accurate species authentication. However, Lamiaceae phylogenetics remain complicated by inconsistencies between morphological and DNA data. This study reconstructed Lamiaceae phylogeny using partial ITS, matK, and rbcL barcodes to evaluate their potential application in species authentication and adulteration prevention. Sequences for 52 species across 11 genera (Spathodea campanulata: outgroup) were obtained from NCBI GenBank, aligned, and trimmed. Four maximum parsimony (MP) trees were constructed in MEGA 11 (three single-barcode, one concatenated). The concatenated dataset was also analyzed by maximum likelihood (ML). Tree robustness was evaluated with bootstrapping, consistency index (CI), and retention index (RI). matK had the longest mean sequence (785.6 bp), rbcL the highest homology (83.5%), and ITS the most parsimony-informative sites (40.3%). MP trees exhibited moderate homoplasy (mean CI = 0.63) but strong synapomorphic signal (mean RI = 0.83). Individual barcodes produced similar genus groupings, yet misplaced several species. Concatenation corrected these positions across MP and ML trees, resolving six robust monophyletic clades (bootstrap >70%), broadly consistent with earlier phylogenies: Callicarpa; Scutellaria; Clerodendrum, Lamium, and Stachys; Salvia; Thymus, Origanum, and Mentha; Orthosiphon and Ocimum. Topological discrepancies with prior studies likely reflect differences in barcode choice and taxon sampling. Concatenated barcodes improved phylogenetic resolution in Lamiaceae, producing clades that identify potential adulterants and guide DNA marker development for species authentication and adulterant detection.

Keywords

DNA barcodes; Lamiaceae; molecular phylogenetics; species authentication

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FWCIfield-weighted

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Percentilevs same year + field

Article

Work type

DIAMOND

Open Access

Topics

Plant Diversity and Evolution Primary

0.14

Ecology, Evolution, Behavior and Systematics › Agricultural and Biological Sciences › Life Sciences

Phytochemistry and Biological Activities

0.13

Wood and Agarwood Research

0.12

Semantic Profile AI-classified research signals

Core Domains

Biology 0.78

level 0

Evolutionary biology 0.50

level 1

DNA barcoding 0.44

level 2

Secondary Topics

Taxon 0.42 Lamiaceae 0.40 Combretaceae 0.36 Mega- 0.36 Zoology 0.34 Barcode 0.29 Genus 0.27 Entomology 0.25

Institution Network

Indonesia University of Education ID
Chayra Endlessa · TOPIK HIDAYAT · Siti Sriyati

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[ref-1] ] Ahmed SM. Molecular identification of Lavendula dentata L., Mentha longifolia (L.) Huds. and Mentha × piperita L. by DNA barcodes. Bangladesh J Plant Taxon. 2018;25(2):149–57. doi: 10.3329/bjpt.v25i2.39519 DOI: 10.3329/bjpt.v25i2.39519

[ref-2] ] The Angiosperm Phylogeny Group IV, Chase MW, Christenhusz MJM, Fay MF, Byng JW, Judd WS, et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc. 2016;181(1):1–20. doi:10.1111/boj.12385 DOI: 10.1111/boj.12385

[ref-3] ] Allkin B. Useful plants – medicines: At least 28,187 plant species are currently recorded as being of medicinal use. In: Willis KJ, editor. State of the world’s plants 2017. London: Royal Botanic Gardens, Kew. 2017. Available from: https://www.ncbi.nlm.nih.gov/books/NBK464488/

[ref-4] ] Uritu CM, Mihai CT, Stanciu GD, Dodi G, Alexa-Stratulat T, Luca A, et al. Medicinal plants of the family Lamiaceae in pain therapy: A review. Pain Res Manag. 2018;2018(1):7801543. doi: 10.1155/2018/7801543 DOI: 10.1155/2018/7801543

[ref-5] ] Zhao F, Chen YP, Salmaki Y, Drew BT, Wilson TC, Scheen AC, et al. An updated tribal classification of Lamiaceae based on plastome phylogenomics. BMC Biol. 2021 Jan;19(2):1–15. doi: 10.1186/s12915-020-00931-z DOI: 10.1186/s12915-020-00931-z

[ref-6] ] Nazar N, Howard C, Slater A, Sgamma T. Challenges in medicinal and aromatic plants DNA barcoding Lessons from the Lamiaceae. Plants. 2022;11(1):137. doi: 10.3390/plants11010137 DOI: 10.3390/plants11010137

[ref-7] ] Thakur VV, Tripathi N, Tiwari S. DNA barcoding of some medicinally important plant species of Lamiaceae family in India. Mol Biol Rep. 2021;48(4):3097–106. doi: 10.1007/s11033-021-06356-3 DOI: 10.1007/s11033-021-06356-3

[ref-8] ] Marieschi M, Torelli A, Bianchi A, Bruni R. Detecting Satureja montana L. and Origanum majorana L. by means of SCAR-PCR in commercial samples of Mediterranean oregano. Food Control. 2011;22(3-4):542–8. doi: 10.1016/j.foodcont.2010.10.001 DOI: 10.1016/j.foodcont.2010.10.001

[ref-9] ] Upton R, David B, Gafner S, Glasl S. Botanical ingredient identification and quality assessment: strengths and limitations of analytical techniques. Phytochem Rev. 2020;19(5):1157–77. doi: 10.1007/s11101-019-09625-z DOI: 10.1007/s11101-019-09625-z

[ref-10] ] Upton R, Dayu RH. Skullcap Scutellaria lateriflora L.: An American nervine. J Herb Med. 2012;2(3):76–96. doi: 10.1016/j.hermed.2012.06.004 DOI: 10.1016/j.hermed.2012.06.004

[ref-11] ] Erickson DL, Driskell AC. Construction and analysis of phylogenetic trees using DNA barcode data. In: Kress W, Erickson D, editors. DNA barcodes: methods in molecular biology. New Jersey: Humana Press; 2012.

[ref-12] Chapter 19. doi: 10.1007/978-1-61779-591-6_19 DOI: 10.1007/978-1-61779-591-6_19

[ref-13] ] Li B, Cantino PD, Olmstead RG, Bramley GLC, Xiang CL, Ma ZH, et al. A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification. Sci Rep. 2016;6(1):34343. doi: 10.1038/ srep34343

[ref-14] ] Aneva I, Zhelev P, Bonchev G, Boycheva I, Simeonova S, Kancheva D. DNA barcoding study of representative Thymus species in Bulgaria. Plants. 2022;11(3):270. doi: 10.3390/plants11030270 DOI: 10.3390/plants11030270

[ref-15] ] Drew BT, Sytsma KJ. Phylogenetics, biogeography, and staminal evolution in the tribe Mentheae (Lamiaceae). Am J Bot. 2012; 99(5):933–53. doi: 10.3732/ajb.1100549 DOI: 10.3732/ajb.1100549

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