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BEIVY JONATHAN KOLONDAM
Department of Biology, Faculty of Mathematics and Natural Sciences, University of Sam Ratulangi, Kampus UNSRAT Bahu, Manado 95115
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Journal : HAYATI Journal of Biosciences

 1 
DNA Barcoding of Sangihe Nutmeg (Myristica fragrans) using matK Gene TRINA EKAWATI TALLEI; BEIVY JONATHAN KOLONDAM
HAYATI Journal of Biosciences Vol. 22 No. 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1458.482 KB) | DOI: 10.4308/hjb.22.1.41

Abstract

Nutmeg (family: Myristicaceae) is a plant that originated from Banda islands and is widely cultivated in several places in the world. Secondary metabolites of this plant have a high value because of their benefits for the health, food, and beauty industries. This study aims at developing DNA barcode for nutmeg (Myristica fragrans) using standard recommended fragment of matK (maturase K) gene. Universal matK primer pairs were used to amplify 889 bp DNA fragment. BLAST search from NCBI site showed that Sangihe nutmeg has 100% identity with Myristica fatua, M. maingayi, and M. globosa. It also has 3 nucleotides difference with Rivola sebifera (identity 99.58%) and 4 nucleotides difference with Knema laurina (identity 99.43%). It can be inferred from this study that single locus of matK gene cannot be used to differentiate species in Myristica; it can only be used to differentiate the genus level within family Myristicaceae.
Integrated DNA Barcoding and Morphometric Characterization of Palm Weevils (Rhynchophorus spp.) in North Sulawesi Balansa, Endrile Golmen; Salaki, Christina Leta; Tarore, Dantje; Mamahit, Juliet Merry Eva; Kolondam, Beivy Jonathan; Tallei, Trina Ekawati
HAYATI Journal of Biosciences Vol. 32 No. 5 (2025): September 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.5.1260-1272

Abstract

Palm weevils (Rhynchophorus spp.) are significant pests of sago palms worldwide. Yet, the taxonomy and evolutionary lineage of these species in North Sulawesi remain unclear, likely due to geographic isolation driving genetic variation and species differentiation. This study aimed to investigate the genetic diversity and morphological differentiation of Rhynchophorus across distinct geographic regions in North Sulawesi using an integrative approach combining DNA barcoding and morphometric analysis. Morphometric traits from palm weevil specimens collected in Sangihe Island, Minahasa, and Bolaang Mongondow were measured and statistically analyzed using one-way ANOVA, MANOVA, principal component analysis (PCA), and linear discriminant analysis (LDA) to assess interpopulation morphological differences. For molecular identification, the cytochrome oxidase I (COI) gene was amplified and sequenced. Phylogenetic relationships were inferred using the maximum likelihood method, and a DNA barcode gap analysis was conducted to evaluate the separation between intra- and interspecific genetic distances. Morphometric analysis revealed significant size variations among the specimens, particularly in rostrum dimensions, with the EBBM (Bolaang Mongondow) group showing the highest values. COI-gene-based identification confirmed that all specimens were of R. vulneratus. However, phylogenetic analysis showed EBMin (Minahasa) and EBBM forming a distinct subgroup, while EBMan, EBSTS, EBTam, and EBSTU (all from Sangihe Island) clustered separately. Barcode gap analysis demonstrated a clear distinction between intra- and interspecific divergence, validating COI as a reliable marker for species delimitation. This study concludes that integrating morphometric and genetic analyses reveals geographic structuring within R. vulneratus, highlighting the effectiveness of combined methods for accurate identification and population differentiation.
Comparative Study of DNA Barcoding and Mini-Barcoding based on COI Gene for Species Identification and Phylogeny of Formicidae Family (Insecta: Hymenoptera) Kolondam, Beivy Jonathan; Tallei, Trina Ekawati; Koneri, Roni; Mamahit, Juliet Merry Eva
HAYATI Journal of Biosciences Vol. 32 No. 6 (2025): November 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.6.1626-1642

Abstract

DNA barcoding and mini-barcoding are widely used to study insect biodiversity, including ants (Hymenoptera: Formicidae). This study evaluated the effectiveness of both approaches for species identification and phylogenetic inference in ants, with particular attention to the performance of universal primers during PCR amplification. Full-length DNA barcode (658 bp) and mini-barcode (127 bp) regions of the mitochondrial cytochrome c oxidase subunit I (COI) gene were retrieved from GenBank, aligned, and analysed with maximum-likelihood phylogenetics (1,000 bootstrap replicates) under the Tamura-Nei model. The universal DNA barcoding primers (Folmer's LCO1490 and HCO2198) showed generally good alignment with ant COI sequences. However, multiple nucleotide mismatches were observed in LCO1490, including one critical mismatch located within the GC clamp region. In contrast, the universal mini-barcoding primers (UniMinibarF1 and UniMinibarR1) showed critical mismatches at their 3′ ends, likely reducing PCR efficiency. Despite limitations associated with primer mismatches, both DNA barcoding and mini-barcoding are reliable for species identification. DNA barcoding and mini barcoding are both capable of distinguishing ants at the species level, regardless of the length of the sequences being compared. The same sequences have also been used for phylogenetic analysis, showing good ability to distinguish ant species based on phylogenetic tree reconstruction. The comparison of DNA barcoding and mini-barcoding in ants showed that longer sequences offered superior resolution for species identification and phylogenetic reconstruction. These findings underscore the need for primer optimisation in ant-specific applications and highlight the utility of both barcoding strategies for taxonomic and evolutionary studies.
Co-Authors Abas, Abdul Hawil Adelfia Papu Agustina Monalisa Tangapo Agustina Tangapo Akihary, Claudia Valleria Arthur G. Pinaria Balansa, Endrile Golmen Bernadus, Zefanya Bernadus, Zefanya G Dantje Tarore Deidy Katili Deidy Yulius Katili Edwin de Queljoe Edy F Lengkong, Edy F Edy Lengkong Eka Julianti Fatimawali . Feky R. Mantiri Fitri Elizabrth Br Hasibuan Indra Polii, Indra J Polii-Mandang J. Polii, Mandang Johanis Pelealu Johanis Pelealu Koneri , Roni Kuron, Sebrina Laksono Trisnantoro Lalu Wahyudi Lisa Ruga Loho, Jesica C. M. Magani, Alce K Makagansa, Marbela Mamahit, Juliet Merry Eva Mangindaan, Glanny Mantang, Wianita Marnix L. D. Langoy Marnix L.D. Langoy Marnix Langoy Meiranty C. Pangerapan, Meiranty C. Mende, Pingkan S. Mende, Pingkan Stela Nelsyani Pasappa Olivia H Abram Pahlevi, Dylan R. Pience Veralyn Maabuat Presticilla D Irawan Presticilla D Irawan Presticilla D Irawan, Presticilla D Roni Koneri Runtunuwu Semuel Runtunuwu, Semuel Salaki, Christina Leta Sari, Nadia Warda Sekar Saroyo Saroyo Singkoh, Marina Flora Oktavine Susan Marlein Mambu Susan Marlein Mambu Tambuwun, Jenifer Timbuleng, Kevin Trina E Tallei Trina E Tallei Trina Ekawati Tallei TRINA EKAWATI TALLEI TRINA EKAWATI TALLEI Umboh, Stella D.