Effectiveness, Sequence Characterization, and DNA QR Code of Internal Transcribed Spacer 1 (ITS1) in Identification of Scopellaria marginata (Cucurbitaceae)
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Abstract
Species identification accurately is crucial in plant sciences. DNA barcoding, which is an accurate approach for molecular identification that involves the use of short and standardized regions such as internal transcribed spacer (ITS1). To date, the availability of barcode sequences for Scopellaria marginata (Cucurbitaceae) is still very limited in public databases including ITS1. The purpose of this study was to investigate the effectiveness, to characterize, and to develop the DNA QR code of ITS1 sequences in the identification of Scopellaria marginata. The DNA barcoding was carried out by DNA extraction from three individual S. marginata, DNA amplification with one pair barcode primer of ITS1, and bi-directional DNA sequencing using the Sanger’s method. Nucleotide composition, phylogenetic tree construction, correct assignment rate (CAR), and DNA QR code were evaluated. The results showed that the ITS1 region in S. marginata with the size of ~290 bp comprises nucleotide composition A, T, G, C, G+C, and A+T content of 23.0%, 17.7%, 26.3%, 33.1%, 59.3%, and 40.7%, respectively. The homology analysis using BLAST and phylogenetic tree reconstruction showed that all samples were identified as S. marginata. The effectiveness of ITS1 as a DNA barcode in the identification of S. marginata showed 100% as the correct assignment rate value. A region of 218 bp was proposed as a specific DNA barcode for S. marginata and also converted as a DNA QR code. Therefore, the ITS1 was shown as an effective barcode for the identification of S. marginata.
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References
Ahmad, A., & Asif, A. (2023). Omics studies of medicinal plants. CRC Press. https://doi.org/10.1201/9781003179139
Aprilianingsih, R., Wahidah, B. F., & Hariri, M. R. (2022). DNA barcode of Homalomena pexa inferred from internal transcribed spacer region. Journal of Biological Research and Its Application, 4(2), 69-74. https://doi.org/10.26740/jrba.v4n2.p69-74
Arslan, M., Tezcan, E., Camci, H., & Avci, M. K. (2021). Effect of DNA concentration on band intensity and resolution in agarose gel electrophoresis. Van Sag Bil Derg, 14(3), 326-333. https://doi.org/10.52976/vansaglik.969547
Arumingtyas, E. L., Turhadi, T., Azrianingsih, R., Afiyanti, M., Pratami, M. P., Sudarjayanti, B. N., & Solihah, F. M. (2023). Rekaman baru Scopellaria marginata (Cucurbitaceae) dari Malang, Jawa Timur, Indonesia. Jurnal Biologi Udayana, 27(2), 183-190.
Chika, S., & Zahro, S, (2024). An in silico approach for evaluation of ITS, rbcL, and psbA-trnH for DNA barcoding of Eugenia spp. Biosfer: Jurnal Tadris Biologi, 15(1), 153-167. http://doi.org/10.24042/biosfer.v15i1.21064
de Boer, H. J., Cross, H. B., de Wilde, W. J. J. J. O., Duyfjes-de Wilde, B. E. E., & Gravendeel, B. (2015). Molecular phylogenetic analyses of Cucurbitaceae tribe Benincaseae urge for merging of Pilogyne with Zehneria. Phytotaxa, 236(2), 173-183. https://doi.org/10.11646/phytotaxa.236.2.6
de Wilde, W. J. J. O., & Duyfjes, B. E. E. (2006). Redefinition of Zehneria and four new related genera (Cucurbitaceae), with an enumeration of the Australasian and Pacific species. Blumea, 51, 1-88.
Dhabal, S., Chakrabarty, A. K., Banerjee, D., Katiyar, C. K., Rai, R. K., & Dubey, S. K. (2024). Internal transcribed spacer (ITS): The powerful DNA barcode and phylogenetic marker for successful authentication of Withania somnifera. Molecular Biology Reports, 52(1), Article 77. https://doi.org/10.1007/s11033-024-10167-7
Hidayat, T., Junior, D., Kusdianti, & Saputro, N. W. (2020). Identifikasi tanaman buah timun apel secara in silico berbasis kode batang DNA. In T. Hidayat, & J. A. Utama (Eds.). Inovasi Matematika, IPA, Komputer, dan Pembelajarannya (pp. 15-25). UPI Press.
Ho, V. T., & Nguyen, M. P. (2020). An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family. Biodiversitas, 21(8), 3879-3885. https://doi.org/10.13057/biodiv/d210858
Hollingsworth, P. M., Graham, S. W., & Little, D. P. (2011). Choosing and using a plant DNA barcode. PLoS ONE, 6(5), Article e19254. https://doi.org/10.1371/journal.pone.0019254
Ilham, M., Mukarromah, S. R., Rakashiwi, G. A., Indriati, D. T., Yoku, B. F., Purnama, P. R., Junairiah, Prasongsuk, S., Purnobasuki, H., & Wahyuni, D. K. (2022). Morpho-anatomical characterization and DNA barcoding of Achillea millefolium L. Biodiversitas, 23(4), 1958-1969. https://doi.org/10.13057/biodiv/d230430
Innis, M. A., Gelfand, D. H., Sninsky, J. J., & White, T. J. (1990). PCR protocols: a guide to methods and applications. Academic Press.
Jiang, S., Chen, F., Qin, P., Xie, H., Peng, G., Li, Y., & Guo, X. (2022). The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants. Physiology and Molecular Biology of Plants, 28(4), 837-848. https://doi.org/10.1007/s12298-022-01175-7
Letsiou, S., Madesis, P., Vasdekis, E., Montemurro, C., Grigoriu, M. E., Skavdis, G., Moussis, V., Koutelidakis, A. E., & Tzakos, A. G. (2024). DNA barcoding as a plant identification method. Applied Sciences, 14(4), Article 1415. https://doi.org/10.3390/app14041415
Li, H., Xiao, W., Tong, T., Li, Y., Zhang, M., Lin, X., Zou, X., Wu, Q., & Guo, X. (2021). The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants. Scientific Reports, 11(1), Article 1424. https://doi.org/10.1038/s41598-021-81087-w
Li, J. F. (2015). A fast neighbor joining method. Genetics and Molecular Research, 14(3), 8733-8743.
Li, X., Yang, Y., Henry, R. J., Rossetto, M., Wang, Y., & Chen, S. (2015). Plant DNA barcoding: from gene to genome. Biological Reviews of the Cambridge Philosophical Society, 90, 157-166. https://doi.org/10.1111/brv.12104
Loera-Sanchez, M., Studer, B., & Kolliker, R. (2020). DNA barcode trnH‑psbA is a promising candidate for efficient identification of forage legumes and grasses. BMC Research Notes, 13(1), Article 35. https://doi.org/10.1186/s13104-020-4897-5
López-Barrera, A., Santos-Ordóñez, E., Pacheco-Coello, R., Villao-Uzho, L., Miranda, M., Gutiérrez, Y., Chóez-Guaranda, I., & Ruiz-Reyes, S. G. (2023). ITS1 barcode and phytochemical analysis by gas chromatography–mass spectrometry of Corynaea crassa Hook. F (Balanophoraceae) from Ecuador and Peru. Genes, 14, Article 88. https://doi.org/10.3390/genes14010088
Lv, Y. N., Yang, C. Y., Shi, L. C., Zhang, Z. L., Xu, A. S., Zhang, L. X., Li, X. L., & Li, H. T. (2020). Identification of medicinal plants within the Apocynaceae family using ITS2 and psbA-trnH barcodes. Chinese Journal of Natural Medicines, 18(8), 594-605. https://doi.org/10.1016/S1875-5364(20)30071-6
Ma, S., Lv, Q., Zhou, H., Fang, J., Cheng, W., Jiang, C., Cheng, K., & Yao, H. (2017). Identification of traditional She medicine Shi-liang tea species and closely related species using the ITS2 barcode. Applied Sciences, 7(3), Article 195. https://doi.org/10.3390/app7030195
Mukhopadhyay, C. S., Choudhary, R. K., & Iquebal, M. A. (2018). Basic applied bioinformatics. John Wiley & Sons, Inc.
Omelchenko, D. O., Krinitsina, A. A., Kasianov, A. S., Speranskaya, A. S., Chesnokova, O. V., Polevova, S. V., & Severova, E. E. (2022). Assessment of ITS1, ITS2, 5’-ETS, and trnL-F DNA barcodes for metabarcoding of Poaceae pollen. Diversity, 14, Article 191. https://doi.org/10.3390/d14030191
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.
Pham, T., Nguyen, Q. T., Tran, D. M., Nguyen, H., Le, H. T., Hoang, Q. T. H., Van, Y. T., & Tran, T. N. (2022). Phylogenetic analysis based on DNA barcoding and genetic diversity assessment of Morinda officinalis How in Vietnam inferred by microsatellites. Genes, 13, Article 1938. https://doi.org/10.3390/genes13111938
Prasetya, E., Prakasa, H., Jannah, M., & Rachmawati, Y. (2020). DNA Barcoding of Edelweiss (Anaphalis longifolia) of North Sumatran origin using sequence maturase K Gene. Jurnal Biosains, 6(3), 115-122. https://doi.org/10.24114/jbio.v6i3.22403
Rohimah, S., Ratnasari, T., & Su’udi, M. (2020). Characteristics of DNA barcodes from three Thrixspermum orchids based on ITS2 regions. Biosaintifika: Journal of Biology & Biology Education, 12(3), 446-452.
Saidon, N. A., Wagiran, A., Samad, A. F. A., Mohd Salleh, F., Mohamed, F., Jani, J., & Linatoc, A. C. (2023). DNA barcoding, phylogenetic analysis and secondary structure predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana. Genes, 14, Article 697. https://doi.org/10.3390/genes14030697
Santosa, B., Darmawati, S., Kartika, A. I., Nuroini, F., Ernanto, A. R., Ayuningtyas, A., Salleh, M. N., & Zulaikhah, S. T. (2020). Isolation, identification similarity and qualitative expression of metallothionein gene in IR-Bagendit rice (Oryza sativa). Pharmacognosy Journal, 12(4), 709-715. https://doi.org/10.5530/pj.2020.12.103
Saudah, Zumaidar, Darusman, Fitmawati, Roslim, D. I., & Juliantari, E. (2022). Molecular authentication of Etlingera spp. (Zingiberaceae) in Aceh Province, Indonesia using DNA barcoding. Biodiversitas, 23(8), 3976-3983. https://doi.org/10.13057/biodiv/d230815
Simpson, M. G. (2019). Plant systematics. (3rd ed). Academic Press.
Stevanus, & Pharmawati, M. (2021). Biodiversity and phylogenetic analyses using DNA barcoding rbcL gene of seagrass from Sekotong, West Lombok, Indonesia. Biodiversitas, 22(1), 50-57. https://doi.org/10.13057/biodiv/d220107
Trisyani, N., & Rahayu, D. A. (2020). DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches. Biodiversitas, 21(2), 478-484. https://doi.org/10.13057/biodiv/d210207
Trivedi, S., Rehman, H., Saggu, S., Panneerselvam, C., & Ghosh, S. K. (2020). DNA barcoding and molecular phylogeny. (2nd ed). Springer.
Turhadi, Sudarjayanti, B. N., Solihah, F. M., Azrianingsih, R., Afiyanti, M., & Arumingtyas, E. L. (2024). Molecular identification of Scopellaria marginata from East Java, Indonesia, based on trnL-UAA and trnL-trnF intergenic spacer regions. Nusantara Bioscience, 16(1), 111-118. https://doi.org/10.13057/nusbiosci/n160114
Turhadi, T., Padmana, I. M. D. R., & Azrianingsih, R. (2025). DNA QR code using Internal transcribed spacer 1 (ITS1) region of commercial cucumber varieties (Cucumis sativus L.). Journal of Biological Research and Its Application, 7(1), 1-7. https://doi.org/10.26740/jrba.v7n1.p1-7
Wang, J., Yan, Z., Zhong, P., Shen, Z., Yang, G., & Ma, L. (2022). Screening of universal DNA barcodes for identifying grass species of Gramineae. Frontiers in Plant Science, 13, Article 998863. https://doi.org/10.3389/fpls.2022.998863
Wang, X. C., Liu, C., Huang, L., Bengtsson-Palme, J., Chen, H., Zhang, J. H., Cai, D., & Li, J. Q. (2015). ITS1: a DNA barcode better than ITS2 in eukaryotes? Molecular Ecology Resources, 15(3), 573-586. https://doi.org/10.1111/1755-0998.12325
Yao, R., Guo, R., Liu, Y., Kou, Z., & Shi, B. (2022). Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding. PLoS ONE, 17(7), Article e0271633. https://doi.org/10.1371/journal.pone.0271633
