Turhadi Turhadi, Briliyan Natalina Sudarjayanti, Brian Rahardi, Estri Laras Arumingtyas
East Java, Indonesia, has been identified as a new distribution area for Scopellaria marginata (Blume) W.J.de Wilde & Duyfjes (Cucurbitaceae) based on morphological evidence. To confirm this finding, molecular validation through DNA barcoding is required for accurate species identification. This study was to analyze the performance of rbcL, matK, and trnK regions in S. marginata identification. The DNA barcoding was performed by genomic DNA extraction from S. marginata, PCR amplification using three regions (rbcL, matK, and trnK), and DNA sequencing. The rbcL, matK, and trnK showed that successfully amplified in all samples with fragment sizes of ~290 bp, ~700 bp, and ~170 bp, respectively. The homology analysis using BLASTn and phylogenetic tree construction based on rbcL and matK showed that all samples were S. marginata species. However, the trnK intron showed ambiguous results. Furthermore, the correct assignment rate value for rbcL and matK were 100%, while trnK was 0% for S. marginata. Two-dimensional DNA barcodes with lengths 261 and 668 bp for rbcL and matK have been proposed as S. marginata-specific barcode which converted into DNA QR code. The rbcL and matK as effective barcodes, while trnK categorized as ambiguous barcode to identify S. marginata. These finding highlights the rbcL and matK as potential DNA barcodes for identification of S. marginata. © 2025 Instituto de Tecnologia do Parana. All rights reserved.
Universitas Brawijaya, Faculty of Mathematics and Natural Sciences, Department of Biology, East Java, Malang, Indonesia
