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Putri, Fatma Jumaita
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Immunology & microbiology

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Multilocus Analysis of matK, atpB-rbcL Intergenic Spacer, and trnL-trnF Intergenic Spacer in Pandanaceae Putri, Fatma Jumaita; Herman, Herman; Roslim, Dewi Indriyani
Jurnal Biologi Tropis Vol. 25 No. 2 (2025): April-Juni
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v25i2.8775

Abstract

Species within the Pandanaceae family, particularly those in the Pandanus genus, exhibit substantial morphological variation, often leading to challenges in accurate species identification. This study conducted a multilocus DNA barcode analysis using sequences of matK, atpB-rbcL Intergenic Spacer (IGS), and trnL-trnF Intergenic Spacer (IGS) obtained from GenBank. Sequence alignment was performed using MAFFT v.7, and the aligned sequences were concatenated into multilocus datasets. Further analyses included frequency data evaluation and phylogenetic tree construction using the Neighbor Joining method in MEGA11. Results revealed that matK had the highest number of conserved sites and the greatest genetic stability, making it particularly effective for identifying broader taxonomic groups. In contrast, atpB-rbcL IGS and trnL-trnF IGS showed greater genetic variation, useful for distinguishing species with similar morphological features. Phylogenetic trees based on single- or two-locus data often failed to group species accurately, while multilocus combinations yielded well-resolved and more reliable tree structures. Therefore, the combined use of atpB-rbcL IGS + matK + trnL-trnF IGS significantly improves species resolution and reduces taxonomic misidentification within Pandanaceae. This study underscores the importance of multilocus barcoding in addressing limitations of morphological classification and enhancing molecular taxonomy in morphologically complex plant groups.
Primer Construction of Transporter Genes Based on Almt1 for The Analysis of Cmp-Sialic Acid Transporter Gene in Derendan Taufikurrahman, Taufikurrahman; Putri, Fatma Jumaita; Nurbaiti, Nurbaiti; Ramadhani, Putri Oktavia; Wahibah, Ninik Nihayatul
Jurnal Biologi Tropis Vol. 25 No. 3 (2025): Juli-September
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v25i3.9069

Abstract

Derendan (Lansium sp.) is an underutilized endemic fruit tree species from Bengkalis Island that grows in acidic peatland soils with high concentrations of toxic aluminum ions (Al³⁺). This study aimed to construct gene-specific primers to detect stress tolerance genes in derendan, with an initial focus on the ALMT1 (Aluminum-activated malate transporter) gene, which is known to mediate aluminum detoxification through organic acid exudation. Primers were designed based on ALMT1 sequences from model species and tested using PCR amplification and sequencing of derendan genomic DNA. Surprisingly, the amplified DNA fragment showed high similarity with CMP-sialic acid transporter 1 genes in several plant species, based on BLASTn analysis. The CMP-sialic acid transporter gene encodes a protein involved in the transport of sialic acid, an organic acid known to play roles in abiotic stress responses. These findings suggest that the constructed primers may target conserved transporter domains related to stress adaptation. The resulting primers have potential applications in molecular studies and breeding programs aimed at enhancing peatland stress tolerance in derendan and related species.
Analysis of matK and trnL-trnF Intergenic Spacer on Pandan (Benstonea sp.) From Kualu Village, Riau Province, Indonesia Nugraha, Fadel; Sofhya, Putri Tri; Putri, Fatma Jumaita; Herman, Herman; Roslim, Dewi Indriyani
Jurnal Biologi Tropis Vol. 25 No. 4a (2025): Special Issue
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v25i4a.10731

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.
Co-Authors Dewi Indriyani Roslim Fadel Nugraha Herman Ninik Nihayatul Wahibah Nurbaiti Nurbaiti Ramadhani, Putri Oktavia Sofhya, Putri Tri Sugeng, Santoso Taufikurrahman Taufikurrahman