Analysis of Three DNA Barcoding (matK, rbcL, ITS) in the Anacardiaceae Family
DOI:
10.29303/jbt.v26i2.11746Published:
2026-05-02Downloads
Abstract
The Anacardiaceae family is a group of tropical plants that have important economic value, but the identification of its species is often hampered by morphological similarities. Molecular approaches through DNA barcoding are an alternative to improve the accuracy of identification and kinship analysis. The purpose of this study was to analyze the combination of three DNA barcodes, namely (matK, rbcL and ITS) in the Anacardiaceae family. The materials used in this study were DNA sequence databases (rbcL, matK, ITS) from the Anacardiaceae family consisting of eight genera and one outgroup used, namely Pometia pinnata, downloaded from GenBank through the NCBI website. Sequences were aligned using MAFFT v.7, edited using BioEdit v.7.2, and analyzed using MEGA 11 to calculate nucleotide frequencies, nucleotide base pairs, diversity, and phylogenetic tree reconstruction using the Neighbor-joining method with 1000 bootstrapping times. The results showed that the matK sequence, a combination of matK+rbcL sequences, and a combination of matK+rbcL+ITS sequences were the most optimal barcodes for grouping species of the same genus in the Anacardiaceae family and separating out-group species. The ITS sequence, a combination of matK+ITS sequences, and a combination of rbcL+ITS sequences were able to group species of the same genus well but could not separate out-group species. The rbcL sequence was not optimal for use as a single DNA barcode.
Keywords:
Anacardiaceae DNA barcode Genetic variation Multilocus phylogeneticsReferences
Adimaka, N., Rifki, M., Dewanti, R. & Cahyadi, M. (2019). Keragaman genetik puyuh Jepang (Coturnix japonica) berdasarkan analisis sekuen DNA mitokondria gen Cytochrome-b. Jurnal Ilmu-lmu Peternakan, 29(2):143-151.
https://doi.org/10.21776/ub.jiip.2019.029.02.05.
Alex, VN., Denisse, T. & Christine, RB. (2021). Hotspots of Human mutation. Trends in Genetics, 37:717-729.
doi:10.1016/j.tig.2020.10.003.
Ariffin, Z., Sah, MD., Idris, S. & Hashim, N. (2015). Genetic diversity of selected mangifera species revealed by inter simple sequence repeats markers. International Journal of Biodiversity, 1–8.
https://doi.org/10.1155/2015/458237.
Aulia, A. (2022). Studi in silico potensi dna barcode berbasis dna kloroplas (Cpdna) untuk identifikasi variasi genetik opuntis sp. Jurnal Syntax Admiration, 3(11):1383- 1394.
https://doi.org/10.46799/jsa.v3i11.512.
CBOL Plant Working Group. (2009). A DNA barcode for land plants. Di dalam: Proceedings of the National Academy of Sciences. USA. hlm. 12794-12797.
https://doi.org/10.1073/pnas.0905845106.
Dwinianti, EF., Ainiyah, D., Afidah, Y & Suudi, M. (2025). DNA barcode analysis of dendrobium sp. based on rbcL sequence. Jurnal Biologis Tropis, 25(4):5795-5803.
doi:10.29303/jbt.v25i4.10177.
Farias, JC., Mayo, SJ., Vieira, IR. & Andrade, IMD. (2024). Using morphometrics to distinguish the restinga and cerrado ecotypes of wild Anacardium occidentale (Anacardiaceae): a preliminary study in northeastern Brazil. Plant Systematics and Evolution, 310(3):1-23.
doi:10.1007/s00606-023-01887-7
Fitmawati, F., Juliantari, E. & Sofiyanti, N. (2017). Phylogenetic study of mangifera central sumatra based on rbcL sequences. Applied Science and Technology, 1(1): 128-131.
Ghorbani, A., Saeedi, Y. & De Boer, HJ. (2017). Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran. PloS One, 12(4):1-15.
https://doi.org/10.1371/journal.pone.0175722.
Guerra, RNM., Oliveira, AS., Farias, JR., Franco, DCG., Santos, PG., Barbosa, NT., Muniz, SB., Abreu, AG. & Nascimento, FRF. (2025). Anacardiaceae family: effect of isolated compounds and other identified phytochemicals against clinically relevant candida species-a short review. Antibiotics 14(308):2-19.
https://doi.org/10.3390/antibiotics14030308.
Hasibuan, F.E., Mantiri, F.R. & Rumende, R.R.H. 2017. Kajian variasi sekunes intraspesies dan filogenetik monyet hitam sulawesi (Macaca nigra) dengan menggunakan gen COI. Jurnal Ilmiah Sains, 17(1): 59-67.
https://doi.org/10.35799/jis.17.1.2017.15558.
Ibrahim, K.S., Gurusubramanian, G., Zothansanga, Yadav, R.P., Kumar, N.S., Pandian, S.K. & Mohan, P.B.S. (2017). Bioinformatics-A Students Companion. Singapore: Bussines Media Singapore.
Katonge, J.H. & Ally, Z.K. (2025). Evolutionary relationships and genetic diversity in the BlaTEM gene among selected gram-negative bacteria. Biochemistry and Biophysics Reports, 42:1-6.
https://doi.org/10.1016/j.bbrep.2025.101985.
Kumar, K., Anjoy, P., Sahu, S., Durgesh, K., Das, A., Tribhuvan, K.U., Sevanthi, A.M., Joshi, R., Jain, P.K., Singh, N.K., Rao, A.R. & Gaikwad, K. (2022). Single trait versus principal component based association analysis for fowering related traits ni pigeonpea. Scientifc Reports, 12(1):1-15.
doi: 10.1038/s41598-022-14568-1.
Latifah, N. & Dharmono. (2018). Keanekaragaman genus dan spesies tumbuhan dari famili anacardiaceae di hutan Pantai Tabanio, Kabupaten Tanah Laut. Di dalam: Prosiding Seminar Nasional Lingkungan Lahan Basah, April 2018. Banjarmasin: Universitas Lambung Mangkurat. Program Studi Magister Pendidikan Biologi FKIP. hlm. 306-310.
https://snllb.ulm.ac.id/prosiding/index.php/snllb-lit/article/view/64.
Lestari, D.A., Azrianingsih, R. & Hnedrian. (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, 3:1-7.
doi:10.22146/jtbb.28308.
Manurung, J., Prakasa, H., Tanjung, U.J. & Harsono, T. (2018). Hubungan kekerabatan spesies dalam genus zanthoxylum menggunakan sekuens gen Maturase K (matK) DNA kloroplas. Jurnal Biosains, 4(2):69-77.
doi:10.24114/jbio.v4i2.10166.
Masruroh, I.H., Triesita, N.I.P., Sulistiono & Santoso, A.M. (2018). Hubungan Kekerabatan Bambu Berdasasarkab Gen rbcL Berbasis Analisis In Silico Sebagai Bukti Adanya Evolusi Molekuler. Didalam: Prosiding Seminar Nasional VI Hayati. Universitas Nusantara PGRI Kediri. Kediri. hlm. 164-178.
https://doi.org/10.29407/hayati.v6i1.650.
Mishra, P., Kumar, A., Nagireddy, A., Mani, D.N., Shuk,la AK., Tiwari, R. & Sundaresan, V. (2015). DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnol Journal, 14(1):8-21.
doi:10.1111/pbi.12419.
Naim, D.M.D., Kamal, N.Z.M. & Mahboob, S. (2020). Population structure and genetic diversity of Aedes aegypti and Aedes albopictus in Penang as revealed by mitochondrial DNA cytochrome oxidase I. Saudi Journal of Biological Sciences, 27:953-967. doi: 10.1016/j.sjbs.2020.01.021.
Perwitasari, D.A.G., Rohimah, S., Ratnasari, T,, Sugiharto, B. & Su’udi, M. (2020). DNA barcoding anggrek obat Dendrobium discolor Lindl. tanimbar menggunakan gen rbcL dan ITS. Buletin Penelitian Tanaman Rempah Dan Obat, 31(1):8-20.
doi:10.21082/bullittro.v31n1.2020.8-20.
Raclariu, A.C., Heinrich, M., Ichim, M.C. & Boer, D.H. (2018). Benefits and limitations of DNA barcoding and metabarcoding in herbal product authentication. Phytochemical Analysis, 29(2):123–128.
doi: 10.1002/pca.2732.
Rahayu, D.A. & Jannah, M. (2019). DNA Barcode Hewan dan Tumbuhan Indonesia. Jakarta: Yayasan Inspirasi Ide Berdaya.
doi:10.17605/OSF.IO/TY7E5.
Risah & Jannah, M. (2025). Studi in silico potensi dna barcode berdasarkan gen matK, ITS, dan rbcL serta analisis filogenetik pada anggrek langka phalaeonopsis. Biotropic The Journal of Tropical Biology, 9(2):11-24.
https://doi.org/10.29080/biotropic.v9i2.2343.
Ryadi, A., Siregar, I., Moura, C.D.M., Gailing, O. & Amandita, F.Y. (2023). An early reference to dna barcode for the anacardiaceae family Journal Of Biosciences, 30(3): 543-550.
https://doi.org/10.4308/hjb.30.3.543-550.
Saputri, R. & Arsyadi, A. (2025). Identifikasi molekuler Pelawan Kepuh (Tristaniopsis obovata Benn.) dari Pulau Bangka berdasarkan gen Internal Transcribed Spacer. Journal of Natural Sciences, 6(3):213-223.
doi:10.34007/jonas.v6i3.1005.
Savadi, S., Muralidhara, B.M., Godwin, J., Adiga, JD., Mohana, GS., Eradasappa, E., Shamsudheen, M. & Karun, A. (2022). De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.). Scientific report, 12(1):1-13.
doi:10.1038/s41598-022-22600-7.
Stansfield, W.D. (2006). Biologi Molekuler dan Sel. Erlangga: Jakarta. ISBN: 9797811913.
Sumarlina, Napitupulu T.S., Nadhirah, A. & Mulyadi, F. (2023). Analisis molekuler tanaman fungsional genus Momordica berdasarkan DNA barcode region matK. Jurnal Agriment, 8(1):51-59.
doi:10.51967/jurnalagriment.v8i1.2543.
Sundari, Khadijah, Jayali, A.M., & Sukamto, N. H. (2019). The application of barcode DNA rbcL gene for identification of medicinal plants: Red jabon and gofasa. Journal of Physics: Conference Series, 1146(1): 1-5.
doi:10.1088/1742-6596/1146/1/012030.
Suudi, M., Ramadany, Z., Rohimah, S., Arum, A.Y., Setyati, D. & Ulum, F.B. (2023a). Peran mini-barcode Internal Transcribed Spacer 2 (ITS 2) untuk identifikasi molekuler spesies Anggrek. Indonesian Journal of Biotechnology and Biodiversity, 7(1):34-45.
https://doi.org/10.47007/ijobb.v7i1.166.
Suudi, M., Ulum, F.B., Ardiyansah, M. & Fitri, N.E. (2023b). Evaluasi lokus potensial matK dan ITS 2 untuk DNA barcoding Anggrek Bulbophyllum lobbii Lindl. AL-KAUNIYAH: Jurnal Biologi, 17(2):406-418.
https://doi.org/10.15408/kauniyah.v17i2.33897.
Tajima, F. (1989). The effect of change in population size on DNA polymorphism. Genetics, 123(3):597-601.
https://doi.org/10.1093/genetics/123.3.597.
Temunovic, M., Sola, Z., Jaksic, F., Vidakovic, A., Liber, Z., Poljak, I. & Bogdanovic, S. (2024). Clarifying genetic and taxonomic relationships among Pistacia taxa (Anacardiaceae) in Croatia. Acta Bot Croat, 83(1):1-13.
https://doi.org/10.37427/botcro-2024-009.
Vertiana, E.V., Oari, A.A. & Hariri, M.R. (2023). Studi perbandingan kode batang DNA inti dan kloroplas pada Heliconia in silico. Jurnal Ilmiah Biologi, 2(2): 39-47.
doi:10.6084/m9.figshare.23564679.
Wardani, I.G.A.K., Amandita, F.Y., de Melo Moura, C.C., Gailing, O. & Siregar, I.Z. (2022). Molecular taxonomy via DNA barcodes for species identification in selected genera of Fabaceae. Jurnal Pengelolaan Sumberdaya Alam Dan Lingkungan, 12(1) 112-122. doi:10.29244/jpsl.12.1.112-122.
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