DNA Barcoding and Taxonomic Placement of Alocasia flemingiana Yuzammi & A. Hay Based on trnL-trnF Intergenic Spacer Region
DOI:
https://doi.org/10.55981/floribunda.2026.15889Keywords:
Aroid, Java, Maximum Likelihood, MEGA 11, PhylogenyAbstract
Siti Latipah, Miftahul Jannah & Muhammad Rifqi Hariri 2026. DNA Barcoding and Taxonomic Placement of Alocasia flemingiana Yuzammi & A. Hay based on trnL-trnF intergenic spacer region. Floribunda 9(1) 27—33 — Alocasia flemingiana Yuzammi & A. Hay is a species of the family Araceae for which molecular data remain limited. The high morphological similarity among Alocasia species often complicates species identification and taxonomic classification. This research tended to characterize the trnL-trnF intergenic spacer (IGS) sequence of A. flemingiana and examine its phylogenetic position employing DNA barcoding. A 450 bp trnL-trnF IGS sequence was successfully amplified and examined. BLAST analysis revealed high sequence similarity with several Alocasia species, with query coverage ranging from 98% to 100%, E-values of 0.0, and percent identities of 99.12% to 100%. The highest similarity was observed with Alocasia sp. PSA280 (100% identity, 98% query coverage), while several accessions of A. longiloba also showed high sequence similarity (>99% identity). Phylogenetic reconstruction using the Maximum Likelihood method under the Tamura 3-parameter model with 1,000 bootstrap replicates placed A. flemingiana in a well-supported clade with A. longiloba (ON777914.1), supported by a bootstrap value of 92%. These results demonstrate that the trnL-trnF IGS region is useful for species identification and phylogenetic inference in Alocasia, while providing molecular evidence supporting the taxonomic placement of A. flemingiana. This study contributes to the molecular characterization of A. flemingiana and highlights the value of DNA barcoding in plant taxonomy and biodiversity research.
Downloads
References
Asih NPS, Purnomo & Daryono BS 2023. Genetic Diversity and Phylogeny of Alocasia Longiloba Miq. Indonesia Accessions based on trnL-F Intergenic Spacer Region. JST (Jurnal Sains Dan Teknologi) 12(2): 485–493.
Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y, Raytselis Y, Sayers EW, Tao T, Ye J & Zaretskaya I 2013. BLAST: a more efficient report with usability improvements. Nucleic Acids Research 41(W1): W29–W33.
Dwivedi B & Gadagkar SR 2009. Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evolutionary Biology 9(1): 211.
Felsenstein J 1985. Confidence Limits on Phylogenies: An Approach Using The Bootstrap. Evolution 39(4): 783–791.
Fitmawati, Desti, Juliantari E, Novela D & Kapli H 2022. Molecular phylogeny of nibung (Oncosperma tigillarium [Jack] Ridl.) inferred from trnL-F intergenic spacer sequences. SABRAO Journal of Breeding & Genetics 54(1): 175–183.
Hay A 1991. The genus Alocasia (Araceae) Australasia. Blumea 35: 449–545.
Hay A 1998. The genus Alocasia (Araceae - Colocasieae) in West Malesia and Sulawesi. Gardens’ Bulletin Singapore 50: 221–334.
Henriquez CL, Arias T, Pires JC, Croat TB & Schaal BA 2014. Phylogenomics of the plant family Araceae. Molecular Phylogenetics and Evolution 75: 91–102.
Imran A, Hasyimuddin H & Nurindah N 2022. Identifikasi jenis tumbuhan talas di Hutan Topidi, Kecamatan Tinggimoncong, Kabupaten Gowa, Sulawesi Selatan. Filogeni: Jurnal Mahasiswa Biologi 2(2): 59–63.
Jain C, Zhang H, Gao Y & Aluru S 2020. On the complexity of sequence-to-graph alignment. Journal of Computational Biology 27(4): 640–654.
Lestari DA, Azrianingsih R & Hendrian H 2018. Filogenetik jenis-jenis Annonaceae dari Jawa Timur koleksi Kebun Raya Purwodadi berdasarkan coding dan non-coding sekuen DNA. Journal of Tropical Biodiversity and Biotechnology 3(1): 1–7.
Lin X, Stur E & Ekrem T 2015. Exploring genetic divergence in a species-rich insect genus using 2790 DNA barcodes. PloS ONE 10(9): e0138993.
Mazlan AH, Najib MHAM, Hassan MH, Mohd Hatta FH & Mohd Yusoff R 2024. Effect of DNA template concentration on standard polymerase chain reaction. International Journal of Pharmaceuticals, Nutraceuticals and Cosmetic Science (IJPNaCS) 7(1): 1–11.
Nisyawati MW & Mustaqim WA 2017. A guide to the urban plants of. UI Publishing. Depok, Indonesia.
Pearson WR 2013. An introduction to sequence similarity (“homology”) searching. Current Protocols in Bioinformatics 42(1): 3–1.
Peninal S, Subramanian J & Kalaiselvam M 2017. Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters. Genomics Data 11: 81–84.
POWO 2026. Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet; https://powo.science.kew.org/ Retrieved 17 June 2026.
Rahayu DA & Jannah M 2019. DNA barcode hewan dan tumbuhan Indonesia. Yayasan Inspirasi Ide Berdaya. Jakarta, Indonesia.
Taberlet P, Gielly L, Pautou G & Bouvet J 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17(5): 1105–1109.
Tamura K 1992. Estimation of the number of nucleotida substitutions when there are strong transition-transversion and G+C-content biases. Molecular Biology and Evolution 9(4): 678–687.
Tamura K, Stecher G & Kumar S 2021. MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38(7): 3022–3027.
Tsai LC, Yu YC, Hsieh HM, Wang JC, Linacre A & Lee JCI 2006. Species identification using sequences of the trnL intron and the trnL-trnF IGS of chloroplast genome among popular plants in Taiwan. Forensic Science International 164(2–3): 193–200.
Yılmaz AYKUT 2025. Primer Design for trnL-trnF IGS Sequences of the Quercus L. Species. Russian Journal of Genetics 61(12): 1627–1635.
Yu H, Chapman B, Di Florio A, Eischen E, Gotz D, Jacob M & Blair RH 2019. Bootstrapping estobservations and model selection. Computational Statistics 34(1): 349–372.imates of stability for clusters,
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Siti Latipah, Miftahul Jannah, Muhammad Rifqi Hariri
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (SeeThe Effect of Open Access).
