Molecular authentication of Etlingera spp. (Zingiberaceae) in Aceh Province, Indonesia using DNA barcoding




Abstract. Saudah, Zumaidar, Darusman, Firmawati, Rislim DI, Juliantari E. 2022. Molecular authentication of Etlingera spp. (Zingiberaceae) in Aceh Province, Indonesia using DNA barcodingBiodiversitas 23: 3976-3983Etlingera spp.or locally known as Etlingera spp.(Acehnese) already has strong basic evidence in the treatment of traditional tribes in Aceh such as cough medicine, fever and sprains, and used to food and spices. Etlingera sppused in various places varies based on morphological characteristics. On the other hand, for the development of phytopharmaceutical, the use of Etlingera sppas plant herb requires authentication about the names. This study aimed to authenticate Etlingera spp. from Aceh using DNA barcoding. Nuclear ITS and trnL-F DNA sequences were used to authenticate among species of Etlingera spp. In this study different species of Etlingera sppcan be differentiated effectively by comparing the DNA barcoding regions. ITS sequence data can identify two different species of Etlingera (E. elatior and E. hemisphaerica). The two identified Etlingera spp.species can be used as important information for further research related to their pharmacological studies. One marker and combined analysis of ITS and trnL-F data proved that the Etlingeraspp. is a monophyletic group and provided phylogenetic information in closely related species. The intraspecific and interspecific variation of ITS markers were more discriminatory regions, while trnL-F IGS were of lower divergences. Our findings indicated that DNA barcoding is efficient and powerful to authenticate herbal medicine Etlingera spp..


Amandita FY, Rembold K, Vornam B, Rahayu S, Siregar IZ, Kreft H, Finkeldey R. 2019. DNA Barcoding of flowering plants in Sumatra, Indonesia. Ecology and Evolution 9 : 1858–1868.
Biswas K, Biswas R. 2014. DNA molecular markers based authentication of herbal drugs-A review. International Journal for Pharmaceutical Research Scholars 3(1) : 581-593.
Burtt BL, Smith RM. 1986. Etlingera: the inclusive name for Achasma, Geanthus and Nicolaia (Zingiberaceae). Notes Roy. Bot. Gard. Edinburgh 43: 235–241.
Chaudhary AA, Ahmad A, Iqbal M. 2014. Molecular biology techniques for authentication of medicinal plants, in: Current trends in medicinal botany, IK International Publishing House, New Delhi. 311-345.
Daniell H, Lin CS, Yu M. 2016. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17: 134,
Danyan Su, Lingxiao Yang, Xuan Shi, Xiaoya Ma, Xiaofan Zhou S. 2021. Hedges B, Bojian Z. Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants. Molecular Biology and Evolution 38(8): 3332–3344.
Farris JS. 1989. The retention index and the rescaled consistency index. Cladistics 5: 417–419
Fitmawati, Hartana A. 2010. Phylogenetic study of Mangifera laurina and its related species uing cpDNA trnLF intergenic spacer markers. Hayati J Biosci 17(1): 9–14.
Ganie SH, Upadhyay P, Das S, PrasadSharma M. 2015. Authentication of medicinal plants by DNA markers. Plant Gene 4: 83-99.
Govindaraj M, Vetriventhan M, Srinivasan M. 2015. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Gen. Res. Int 1: 14.
Greiner S, Sobanski J, Bock R. 2015. Why are most organelle genomes transmitted maternally?, Bioessays 37(1): 80-94.
Hapsari L, Azrianingsih R, Arumingtyas EL. 2018. Genetic variability and relationship of banana cultivars (Musa l.) from East Java, Indonesia based on the internal transcribed spacer region nrDNA sequences. J Trop Biol Conserv 15(1): 101-120.
Hasegawa M, Kishino H, Yano T. 1985. Dating of Humanape Splitting by A Molecular Clock of Mitochondrial DNA. Evolution 22(2): 160-174.
Hertweck KL, Kinney MS, Stuart SA, Maurin O, Mathews S, Chase MW, Gandolfo M, Pires JC. 2015. Phylogenetics, divergence times and diversification from three genomic partitions in monocots. Botanical Journal of the Linnean Society 178(3): 375–393.
Ibrahim H, Setyowati FM. 1999. Etlingera. In: Plant Resources of South-East Asia No. 13: Spices. Leiden, The Netherlands: Backhuys Publisher 123-126.
Jackie T, Haleagrahara N, Chakravarthi S. 2011. Antioxidant effects of Etlingera elatior flower extract against lead acetate-induced perturbations in free radical scavenging enzymes and lipid peroxidation in rats. BMC Research Notes 4 : 67.
Klingenberg CP, Gidaszewski NA. 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Syst Biol 59 (3): 245–261.
Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102(23): 8369-8374.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6): 1547-1549.
Larsen K. 1999. Gingers of Peninsular Malaysia And Singapore. Natural History Publications. Malaysia.
Madden T. 2013. The NCBI Handbook, 2 nd edition. National Center for Biotechnology Information (US), Bethesda (MD).
Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R. 2016. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnol. J 14: 8–21.
Pedersen LB. 2004. Phylogenetic analysis of the subfamily Alpinioideae (Zingiberaceae), particularly Etlingera Giseke, based on nuclear and plastid DNA. Plant Syst. Evol 245:239–258.
Rai PS, Bellampalli R, Dobriyal RM, Agarwal A, Satyamoorthy K, Narayana DBA. 2012. DNA barcoding of authentic and substitute samples of herb of the family Asparagaceae and Asclepiadaceae based on the ITS2 region. J. Ayurveda Integr. Med 3: 136-140
Ravindran PN. The encyclopedia of herbs & spices. Volumes 1 and 2. Wallingford, UK: CAB International.xlv + 1128-2017. pp.
Saudah, Ernilasari, Fitmawati, Roslim DI, Zumaidar, Darusman, Monalisa, Umam AH. 2021a. A phytochemical screening of Bak kala (Etlingera elatior) originated from suakbugis, Aceh, Indonesia and its potential in ethnobotany. International Journal of Herbal Medicine 9(4): 37-42.
Saudah, Fitmawati, Roslim, DI, Zumaidar, Darusman, Ernilasari 2021b. Ethnobotany Etlingera elatior (Jack) R.M. Smith (Cikala) in Ethinc Gayo. Advances in Biological Sciences Research 14: 205-209.
Small RL, Cronn RC, Wendel JF. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot 17: 145-170.
Smith RM. 1986. New combinations in Etlingera Giseke (Zingiberaceae). Notes Roy. Bot. Gard. Edinburgh 43: 243–245.
Soltis PS, Folk RA, Soltis DE, Darwin. 2019. Review: angiosperm phylogeny and evolutionary radiation. Proc. Biol. Sci 286 (1899): 1-14.
Soltis PS, Soltis, DE 2003. Applying the bootstrap in phylogeny reconstruction. Stat Sci 18(2): 256–267.
Srivastava S, Sanchita, Bhargava M, Sharma A. 2016. DNA Barcoding of Medicinal Plants. in Medicinal Plants -Recent Advances in Research and Development, Tsay Hsin-Sheng, Shyur Lie-Fen, Agrawal Dinesh Chandra, Wu Yang-Chang, and Wang Sheng-Yang Eds. Singapore: Springer Singapore 97-127.
Su C, Wong KL, But PH, Su, WW, Shaw PC (2010). Molecular authentication of the Chinese herb Huajuhong and related medicinal material by DNA sequencing and ISSR markers. J. Food Drug. Anal 18 (3): 161–170.
Swofford DL. 2002. PAUP*, Phylogenetic Analysis Using Parsimony (*and Other Methods). Versi 4.0b10. Sunderland, MA: Sinauer Associates.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol 30: 2725-2729.
Vassou SL, Kusuma G, Parani, M. 2015. DNA barcoding for species identification from dried and powdered plant parts: a case study with authentication of the raw drug market samples of . Sida cordifolia. Gene 559: 86-93
Wen-Liu Z, Gao YZ, Zhou J. 2019. Molecular authentication of the medicinal species of Ligusticum (Ligustici rhizoma et radix, “gao-ben”) by integrating non-coding internal transcribed spacer 2 (ITS2) and its secondary structure. Frontiers in Plant Science 10 (429): 1-10.
White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: M. Innis, D. Gelfand, J. Sninsky, T. White, eds., PCR protocols: a guide to methods and applications. Academic Press, San Diego, CA.
Zhang W, Yuan Y, Yang S, Huang JJ, Huang LQ. 2015. ITS2 secondary structure improves discrimination between medicinal “Mu Tong” species when using DNA barcoding. PLoS One 10: 131-185.
Zhou J, Wang W, Liu M, Liu Z. 2014. Molecular authentication of the traditional medicinal plant Peucedanum praeruptorum and its substitutes and adulterants by DNA - barcoding technique. Pharmacogn. Mag 10: 385-390.
Zhu RW, Li YC, Zhong DL, Zhang JQ. (2017). Establishment of the most comprehensive ITS2 barcode database to date of the traditional medicinal plant rhodioloa (Crassulaceae). Sci. Rep pp. 7 : 10051.