Comparative evaluation of chloroplast DNA barcoding markers for authenticating ethnomedicinal plants from Surigao del Sur, Philippines
Article Sidebar
Abstract Views: 221
File Views: 124
Main Article Content
Abstract
Abstract. Blasco FA, Raterta R, Alejandro GJD. 2025. Comparative evaluation of chloroplast DNA barcoding markers for authenticating ethnomedicinal plants from Surigao del Sur, Philippines. Biodiversitas 26: 5195-5203. Traditional medicine utilizing ethnomedicinal plants remains crucial for healthcare in developing countries, with authentication being critical for safety and efficacy. DNA barcoding offers a molecular solution for accurate species identification, particularly important for poorly documented flora in biodiversity hotspots. This study evaluated the performance of four chloroplast DNA barcoding regions (rbcL, matK, trnL-F, and trnH-psbA) for authenticating ethnomedicinal plants from the biodiverse Surigao del Sur mountain range, Philippines. This represents the first comprehensive molecular reference dataset for Surigao del Sur ethnomedicinal flora. Fresh leaf samples from 50 ethnomedicinal plant species representing 43 genera and 31 families were collected from three municipalities (Lanuza, Tago, and Tandag). Barcode performance of the four markers was assessed based on PCR success, sequencing quality, BLAST identification accuracy, genetic distance analysis, and phylogenetic reconstruction. The trnH-psbA region achieved the highest PCR amplification success (100%), while trnL-F exhibited optimal balanced performance with 94% PCR success rate. BLAST analysis revealed trnL-F had the highest identification rate (80%), followed by trnH-psbA (66%). The matK showed optimal species-level discrimination with 0.7% intra-generic divergence and achieved strong bootstrap support in phylogenetic analysis. The multi-locus approach combining trnL-F, trnH-psbA, and matK achieved 86% identification success rate. This study contributes 107 novel sequences and provides essential molecular tools for reliable species authentication, supports conservation of ethnomedicinal plant diversity in the Philippines, and establishes a foundation for quality control in traditional medicine practice and international trade.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Arshed MJC, Valdez Jr MB, Alejandro GJD. 2017. Evaluating the feasibility of five candidate DNA barcoding loci for Philippine Lasianthus Jack (Lasiantheae: Rubiaceae). Pharmacogn Mag 13 (52): 553-558. DOI: 10.4103/pm.pm_1_17.
Belgica THR, Suba MD, Alejandro GJD. 2024. Short Communication: Botanical assessment and conservation status of medicinal plants in mountain range of Malinao Albay, Philippines. Biodiversitas 25 (4): 1413-1419. DOI: 10.13057/biodiv/d250409.
Blasco FA, De Guzman GQ, Alejandro GJD. 2014. A survey of ethnomedicinal plants in Surigao del Sur mountain range, Philippines. Intl J Pure Appl Biosci 2 (4): 166-172.
Cabelin VLD, Alejandro GJD. 2016. Efficiency of matK, rbcL, trnH-psbA, and trnL-F (cpDNA) to molecularly authenticate Philippine ethnomedicinal Apocynaceae through DNA barcoding. Pharmacogn Mag 12: S384-S388. DOI: 10.4103/0973-1296.185780.
Cahyaningsih R, Compton LJ, Rahayu S, Brehm JM, Maxted N. 2022. DNA barcoding medicinal plant species from Indonesia. Plants 11 (10): 1375. DOI: 10.3390/plants11101375.
CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proc Natl Acad Sci USA 106: 12794-12797. DOI: 10.1073/pnas.0905845106.
Cordero CS, Guillergan LR, Nievales MFJ, Alejandro GJD. 2025. Ethnobotanical study of medicinal plants used in an urban community in Iloilo City, Philippines. Biodiversitas 26 (5): 2167-2181. DOI: 10.13057/biodiv/d260515.
Cordero CS, Ligsay A, Alejandro GJD. 2020. Ethnobotanical documentation of medicinal plants used by the Ati tribe in Malay, Aklan, Philippines. J Complement Med Res 11 (1): 170-198. DOI: 10.5455/jcmr.2020.11.01.20.
Cordero CS, Meve U, Alejandro GJD. 2022a. Ethnobotanical documentation of medicinal plants used by the indigenous Panay Bukidnon in Lambunao, Iloilo, Philippines. Front Pharmacol 12: 790567. DOI: 10.3389/fphar.2021.790567.
Cordero CS, Meve U, Alejandro GJD. 2022b. Quantitative ethnobotanical documentation of medicinal plants used by the indigenous Ati tribes in Panay Island, Philippines. Malays J Sustain Environ 9 (2): 143-170. DOI: 10.24191/myse.v9i2.18832.
Cordero CS, Meve U, Alejandro GJD. 2023. Ethnobotany and diversity of medicinal plants used among rural communities in Mina, Iloilo, Philippines: A quantitative study. J Asia-Pac Biodivers 16 (1): 96-117. DOI: 10.1016/j.japb.2022.12.003.
de Leon Suba M, Arriola AH, Alejandro GJD. 2019. Evaluation of cpDNA barcodes in selected medicinal plants of Mt. Arayat National Park, Pampanga, the Philippines. J Young Pharm 11 (2): 130-135. DOI: 10.5530/jyp.2019.11.29.
Harris CS, Kim DY, Jordan CR, Miranda MI, Hellberg RS. 2024. DNA barcoding of herbal supplements on the US commercial market associated with the purported treatment of COVID-19. Phytochem Anal 35 (4): 664-677. DOI: 10.1002/pca.3320.
Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc Biol Sci 270 (1512): 313-321. DOI: 10.1098/rspb.2002.2218.
Hughes CE, Eastwood RJ, Bailey CD. 2006. From famine to feast? Selecting nuclear DNA sequences for plant species-level phylogenetic analyses. Philos Trans R Soc B: Biol Sci 361 (1465): 211-225. DOI: 10.1098/rstb.2005.1735.
Ilagan VAD, Alejandro GJD, Paraguison DJB, Perolina SMW, Mendoza GR, Bolina AB, Raterta R, Vales MB, Suarez GJD, Blasco FA. 2022. Ethnopharmacological documentation and molecular authentication of medicinal plants used by the Manobo and Mamanwa tribes of Surigao del Sur, Philippines. Biodiversitas 23 (6): 3185-3202. DOI: 10.13057/biodiv/d230646.
Kolter A, Gemeinholzer B. 2021. Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases. Genome 64 (3): 265-298. DOI: 10.1139/gen-2019-0198.
Letsiou S, Madesis P, Vasdekis E, Montemurro C, Grigoriou ME, Skavdis G, Moussis V, Koutelidakis AE, Tzakos AG. 2024. DNA barcoding as a plant identification method. Appl Sci 14 (4): 1415. DOI: 10.3390/app14041415.
Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. 2015. Plant DNA barcoding: From gene to genome. Biol Rev Camb Philos Soc 90 (1): 157-166. DOI: 10.1111/brv.12104.
Lola AMA, Binag SDA, Alfeche NKG, Alejandro GJD. 2025. DNA barcoding and high-performance liquid chromatography as golden standards of authentication in Blumea balsamifera and Ehretia microphylla products. Biodiversitas 26 (3): 1258-1270. DOI: 10.13057/biodiv/d260325.
Meñiza JF, Pasco MM, Alimbon JA. 2024. A review of ethnobotanical studies reveals over 500 medicinal plants in Mindanao, Philippines. Plant Divers 46 (5): 551-564. DOI: 10.1016/j.pld.2024.05.001.
Naive MAK, Binag SDA, Alejandro GJD. 2021. Plants with benefits: Ethnomedicinal plants used by the Talaandig tribe in Portulin, Pangantucan, Bukidnon, Philippines. Indian J Tradit Knowl 20 (3): 754-766. DOI: 10.56042/ijtk.v20i3.26584.
Nanni L, Cuza D, Brahnam S. 2024. AI-powered biodiversity assessment: Species classification via DNA barcoding and deep learning. Technologies 12 (12): 240. DOI: 10.3390/technologies12120240.
Nazar N, Howard C, Slater A, Sgamma T. 2021. Challenges in medicinal and aromatic plants DNA barcoding—lessons from the Lamiaceae. Plants 11 (1): 137. DOI: 10.3390/plants11010137.
Nazar N, Saxena A, Sebastian A, Slater A, Sundaresan V, Sgamma T. 2025. Integrating DNA barcoding within an orthogonal approach for herbal product authentication: A narrative review. Phytochem Anal 36 (1): 7-29. DOI: 10.1002/pca.3466.
Olsson S, Giovannelli G, Roig A, Spanu I, Vendramin GG, Fady B. 2022. Chloroplast DNA barcoding genes matK and psbA-trnH are not suitable for species identification and phylogenetic analyses in closely related pines. iForest Biogeosci For 15: 141-147. DOI: 10.3832/ifor3913-015.
Paraguison LD, Tandang DN, Alejandro GJD. 2020. Medicinal plants used by the Manobo tribe of Prosperidad, Agusan del Sur, Philippines: An ethnobotanical survey. Asian J Biol Life Sci 9 (3): 326-333. DOI: 10.5530/ajbls.2020.9.49.
R Core Team. 2021. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
Riza LS, Zain MI, Izzuddin A, Prasetyo Y, Hidayat T, Samah KAFA. 2023. Implementation of machine learning in DNA barcoding for determining the plant family taxonomy. Heliyon 9 (10): e20161. DOI: 10.1016/j.heliyon.2023.e20161.
Santor PJR, Ordas JAD, Olivar JEC, Bangcaya PS, Nonato MG, Alejandro GJD. 2021. DNA barcoding of six ethnomedicinal and economically important Pandanus Parkinson (Pandanaceae) in the Philippines. Philipp J Sci 150 (5): 1321-1335. DOI: 10.56899/150.05.39.
Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 38 (7): 3022-3027. DOI: 10.1093/molbev/msab120.
Urumarudappa SKJ, Tungphatthong C, Jaipaew J, Pornputtapong N, Pakdeesattayapong D, Vimolmangkang S, Sukrong S. 2022. Development of a DNA barcode library of plants in the Thai Herbal Pharmacopoeia and monographs for authentication of herbal products. Sci Rep 12 (1): 9624. DOI: 10.1038/s41598-022-13287-x.
WHO [World Health Organization]. 2019. WHO Global Report on Traditional and Complementary Medicine 2019. World Health Organization, Geneva, Switzerland.
Yang C-H, Wu K-C, Chuang L-Y, Chang H-W. 2022. DeepBarcoding: Deep learning framework for species classification using DNA barcoding. IEEE/ACM Trans Comput Biol Bioinform 19 (4): 2158-2165. DOI: 10.1109/TCBB.2021.3056570.
Yu J, Wu X, Liu C, Newmaster S, Ragupathy S, Kress WJ. 2021. Progress in the use of DNA barcodes in the identification and classification of medicinal plants. Ecotoxicol Environ Saf 208: 111691. DOI: 10.1016/j.ecoenv.2020.111691.
Zhu S, Liu Q, Qiu S, Dai J, Gao X. 2022. DNA barcoding: An efficient technology to authenticate plant species of traditional Chinese medicine and recent advances. Chin Med 17 (1): 112. DOI: 10.1186/s13020-022-00655-y.