Analysis of matK and trnL-trnF Intergenic Spacer on Pandan (Benstonea sp.) From Kualu Village, Riau Province, Indonesia

Fadel Nugraha; Putri Tri Sofhya; Fatma Jumaita Putri; Herman Herman; Dewi Indriyani Roslim

doi:10.29303/jbt.v25i4a.10731

Analysis of matK and trnL-trnF Intergenic Spacer on Pandan (Benstonea sp.) From Kualu Village, Riau Province, Indonesia

Authors

Fadel Nugraha , Putri Tri Sofhya , Fatma Jumaita Putri , Herman , Dewi Indriyani Roslim

DOI:

10.29303/jbt.v25i4a.10731

Published:

2025-12-10

Issue:

Vol. 25 No. 4a (2025): Special Issue

Keywords:

Benstonea sp., DNA barcoding, matK, Riau, trnL-trnF intergenic spacer.

Articles

Downloads

How to Cite

Nugraha, F., Sofhya, P. T., Putri, F. J., Herman, H., & Roslim, D. I. (2025). Analysis of matK and trnL-trnF Intergenic Spacer on Pandan (Benstonea sp.) From Kualu Village, Riau Province, Indonesia. Jurnal Biologi Tropis, 25(4a), 535–542. https://doi.org/10.29303/jbt.v25i4a.10731

Download Citation

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

Abstract

Molecular characterization using DNA barcodes is essential for clarifying taxonomic relationships and confirming species identity within the genus Benstonea. Pandan (Benstonea sp.) has potential as a source of bioactive compounds, a subject of genetic and taxonomic studies, and a component of biodiversity that supports conservation and the development of tissue culture for secondary metabolite production. This study aims to analyze the DNA barcode regions matK and trnL-trnF intergenic spacer (IGS) on Benstonea sp. collected from Kualu Village, Riau Province, Indonesia. The fresh leaves of this plant were used for DNA extraction using the Geneaid Mini Plant kit, PCR following Thermo Scientific protocols, agarose gel electrophoresis, sequencing, and data analysis using BioEdit, BLASTn, and MEGA 11.0. In this study had been obtained DNA sequences of matK and trnL-trnF IGS with the size of 846 bp and 964, respectively. Based on BLASTn analysis of the sequences, it showed that the pandan species originating from Kualu Village (Kampar Regency) and Langgam Village (Pelalawan Regency) have similarities with accessions from other genera of the Pandanaceae family (average query cover value reaches 100%). Phylogenetic analysis of the trnL-trnF IGS showed that the pandan plants studied were in the same group as Benstonea sp. 'Kajuik Lake' DIR01 and were clearly separated from the Pandanus and Martellidendron groups. The trnL-trnF IGS can be used to differentiate and group species of the genera Benstonea and Pandanus into distinct clades, whereas the matK was only effective for classification at the genus level. The sequences were submitted to GenBank and were available for use in the molecular identification of this plant.

References

Hanifa, A., Roslim, D.I., & Andariyusti, F. (2021). Identifikasi Molekuler Jeruk Nipis Tegal Berdasarkan Fragmen Gen 18S Ribosomal RNA. Jurnal Bioteknologi dan Biosains Indonesia. 8(2):245–253.

Mursyidin, D.H., Irfan, M. (2020). Keanekaragaman dan kekerabatan genetic Artocarpus berdasarkan penanda DNA kloroplas matK dan rbcL: kajian in silico. Floribunda 6(5): 195-206. DOI: https://doi.org/10.32556/floribunda.v6i5.2020.322.

Parinding, Z. (2021). Identifikasi Jenis-Jenis Pandanaceae di Pulau Pepaya pada Kawasan Taman Nasional Teluk Cenderawasih (Identification of Pandanaceae types in Pepaya Island in the National Park Areas of Teluk Cenderawasih). SCIENCE.1(1):13. DOI:https://doi.org/10.51878/science.v1i1.180.

Roslim, D.I. (2017). Identification of pandan plant (Benstonea sp.) from Riau, Indonesia using theree DNA barcodes. Sabrao Journal. 49(4): 346-360.

Roslim, D.I. (2019). Analysis of matK, rbcL and trnL-trnF Intergenic Spacer Sequences on Durik-Durik (Syzygium sp). J. Phys.: Conf. Ser. 1351 (2019) 012023. DOI:10.1088/1742-6596/1351/1/012023

Roslim, D.I., Asih, H., Herman. (2020). Sekuen DNA Parsial dari Gen gapdh pada Tumbuhan Sirsak (Annona muricata L.). Al-Kauniyah. 13(2): 209-217. DOI: ttp://dx.doi.org/10.15408/kauniyah.v13i2.13964.

Roslim, D.I. & Fitriani, A., (2021). Barkoding DNA pada Tumbuhan Durik-Durik (Syzygium sp.) Asal Riau Menggunakan Daerah Gen ndhF. Jurnal BIOS Logos, 11(1).DOI:https://doi.org/10.35799/jbl.11.1.2021.31191.

Roslim, D.I., Nuraini, I.S., Nurhayati, I., Sianturi, C.V., Thahirah, A., & Herman. (2023). Analisis Empat Sekuen Barkode DNA pada Pandan (Benstonea sp.) Asal Danau Kajuik, Riau. Al-Kauniyah. 16(1):98-114. DOI: http://dx.doi.org/10.15408/kauniyah.v16i1.21697.

Roslim, D.I., Herman, Budiono, D.Y.F, Cahyati, I,E., Lestari, W., Novita, Linda., Priyadi, A. (2024). Analysis of trnL-trnL-trnF intergenic spacer and matK sequences combined with morphological observations showed pucuk seminyak from Riau is Champereia manillana var. manillana Merr. Journal of Tropical Life Science, 14(3): 575–584. DOI: https://doi.org/10.11594/jtls.14.03.13.

Saif, R., Nadeem, S., Khaliq, A., Zia, S., & Iftekhar, A. (2022). Mathematical understanding of sequence alignment and phylogenetic algorithms: A comprehensive review of computation of different methods. Advancements in Life Sciences. 9(4). DOI: https://doi.org/10.62940/als.v9i4.1098.

Sisillia, L., Sabalaka, S. & Kartikawati, S.M., (2024). Kajian pemanfaatan jenis-jenis Pandanus (Pandanaceae) oleh masyarakat Desa Nanga Keruap Kabupaten Melawi. Jurnal Hutan Lestari. 12(1). pp.22–34. DOI:https://doi.org/10.24233/biov.8.2.2022.185.

Tanzerina, N., Harmida, H. & Apriliani, D. (2022). Ethnobotanical study of Pandanaceae by the Besemah tribe, Lahat District, South Sumatera Province: Ethnobotany Pandanaceae. BIOVALENTIA: Biological Research Journal. 8(2):130–137. DOI:10.24233/biov.8.2.2022.185.

Xi Z, Liu L, Davi CC. (2015). Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased. Mol Phylogenet Evol. 92: 63–71. DOI: 10.1016/j.ympev.2015.06.009.

License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Jurnal Biologi Tropis is licensed under a Creative Commons Attribution 4.0 International License.

The copyright of the received article shall be assigned to the author as the owner of the paper. The intended copyright includes the right to publish the article in various forms (including reprints). The journal maintains the publishing rights to the published articles.

Authors are permitted to disseminate published articles by sharing the link/DOI of the article at the journal. Authors are allowed to use their articles for any legal purposes deemed necessary without written permission from the journal with an acknowledgment of initial publication to this journal.

Most read articles by the same author(s)

Muhamad Fauzan, Dewi Indriyani Roslim, Anna Safarrida, Herman Herman, Wahyu Lestari, Effect of Drying Methods on the Total Phenolic of Maman Plant (Cleome gynandra L.) from Riau , Jurnal Biologi Tropis: Vol. 24 No. 2 (2024): April - Juni
Fatma Jumaita Putri, Herman Herman, Dewi Indriyani Roslim, Multilocus Analysis of matK, atpB-rbcL Intergenic Spacer, and trnL-trnF Intergenic Spacer in Pandanaceae , Jurnal Biologi Tropis: Vol. 25 No. 2 (2025): April-Juni
Sri Pujiati, Adiwirman Adiwirman, Herman Herman, Physiological Responses and Agronomic Characters of Local Rice (Oryza sativa L.) Varieties from Rokan Hilir to Salinity (NaCl) Stress , Jurnal Biologi Tropis: Vol. 25 No. 4b (2025): Special Issue
Frederika Sinuraya, Dewi Indriyani Roslim, Deviona Deviona, Suharyanto Suharyanto, The Effect of Colchicine Concentration and Immersion Time on Growth and Morphological Characters of Acacia crassicarpa A. Cunn. Ex Benth In-vitro Explants , Jurnal Biologi Tropis: Vol. 23 No. 3 (2023): July - September
Fadel Nugraha, Michelle Graciella Jacinta Halim, Naomi Chiko Putri Sihotang, Yudha Febrianto, Safniyeti Safniyeti, Nindya Wulandari, Effectiveness of Non-SLS Shampoo Based on VCO and Tectona grandis Leaf Extract for Alopecia Treatment , Jurnal Biologi Tropis: Vol. 25 No. 3 (2025): Juli-September
Miftahul Rahmah, Aldy Riau Wansyah Hasibuan, Tisha Melia, Hapiz Al Khairi, Dewi Indriyani Roslim, DNA Barcoding Analysis of Betok Fish (Anabas testudineus) from Kampar, Riau Based on Cytochrome Oxidase Subunit I (COI) , Jurnal Biologi Tropis: Vol. 24 No. 2 (2024): April - Juni
Taufikurrahman Taufikurrahman, Fatma Jumaita Putri, Nurbaiti Nurbaiti, Putri Oktavia Ramadhani, Ninik Nihayatul Wahibah, Primer Construction of Transporter Genes Based on Almt1 for The Analysis of Cmp-Sialic Acid Transporter Gene in Derendan , Jurnal Biologi Tropis: Vol. 25 No. 3 (2025): Juli-September
Herman Herman, Mayang Sari, Nella Multivasari, Dewi Indriyani Roslim, DNA Barcoding Analysis Kitolod (Hippobroma longiflora) from Riau Based on matk Gene , Jurnal Biologi Tropis: Vol. 25 No. 1 (2025): Januari - Maret
Roza Elvyra, Rio Riduan, Dewi Indriyani Roslim, Molecular Characterization of Danau Selais Fish (Ompok hypophthalmus) and Kaporeh Selais Fish (Ompok eugeneiatus) from Riau Province of Indonesia using Mitochondrial 12S rRNA , Jurnal Biologi Tropis: Vol. 23 No. 1 (2023): Special Issue
Nurbaiti Nurbaiti, Dewi Roslim, Herman Herman, A DNA Barcoding Multilocus Analysis in the Cucurbitaceae Family , Jurnal Biologi Tropis: Vol. 25 No. 2 (2025): April-Juni

1 2 > >>

Analysis of matK and trnL-trnF Intergenic Spacer on Pandan (Benstonea sp.) From Kualu Village, Riau Province, Indonesia

Authors

DOI:

Published:

Issue:

Keywords:

Articles

Downloads

How to Cite

Downloads

Metrics

Abstract

References

License

Most read articles by the same author(s)

Similar Articles

Menu

Manuscript Template

visitor

Keywords

Mitra Kerja sama

Open Access Journals

Contact Us

Information

Share & Follow