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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences
Bayu Pranata
Department of Fisheries, Faculty of Fisheries and Marine Science, University of Papua
Earth & Planetary Sciences

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DNA Barcoding of Snapper Fish (Lutjanus spp.) from Kaimana and Fakfak, West Papua Destia Fitri Ariyani; Wahyu Endra Kusuma; Bayu Pranata; Emmanuel Manangkalangi; Jeni Jeni; Abdul Hamid A. Toha; Muhammad Dailami
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 31, No 1 (2026): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.31.1.26-36

Abstract

Kaimana and Fakfak are two regions in West Papua which have high biodiversity. The total fish production in Kaimana and Fakfak are 10,039 tons.y-1 and 17,806 tons.y-1, respectively. The snapper fish (Lutjanus spp.) is one of the important economic commodities in Kaimana and Fakfak regions. There has been a decrease in the number of exports of snapper fish in 2018 to 2019 from 4,742 tons to 4,290 tons due to overfishing and environmental pollution. This study employed DNA barcoding technology to identify the species of snapper fish collected from Kaimana and Fakfak. The DNA isolation was conducted by using genomic DNA mini kit (tissue) and the amplification of COI gene with Go Taq green master mix. Agarose gel electrophoresis was used to visualize the PCR product.  A total of 16 sequences with length 654 base pairs of COI gene were identified as five species of Lutjanidae, which were Lutjanus decussatus, L. gibbus, L. quinquelineatus, L. malabaricus, and L. johnii. Homology analysis with BLAST NCBI and BOLD System showed that all samples have similarity of 99.08-100% and query cover of 93-100%. Relationship analysis using phylogenetic tree and genetic distances showed results of intraspecific close relatives (0.001-0.016) and interspecific distant relatives (>0.1000). The phylogenetic tree illustrated that all species of Lutjanidae are separated into monophyletic clades. DNA barcoding technology successfully identified the snapper fish collected from Kaimana and Fakfak. 
Diversity of Scombridae in Cenderawasih Bay, Papua, as Revealed by DNA Barcoding Bayu Pranata; Abdul H.A. Toha; Dwi Muhammad Maulana; Robi Binur; Muhammad Dailami; Esie Mega Wangi; Yerri D Mundoni; Sipriyadi Sipriyadi; Aradea Bujana Kusuma
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 31, No 3 (2026): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.31.3.323-332

Abstract

The family Scombridae comprises economically important pelagic fishes traded across. However, taxonomic knowledge of Scombridae in Cenderawasih Bay remains remarkably limited. This study applied DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene for species taxonomy resolution. A total of 57 specimens were successfully sequenced and identified through BLAST against the NCBI database. We detected 12 species from 9 genera, namely Auxis thazard, Katsuwonus pelamis, Euthynnus affinis, Thunnus albacares, Acanthocybium solandri, Scomberomorus commerson, Gymnosarda unicolor, Grammatorcynus bilineatus, Thunnus obesus, Rastrelliger kanagurta, Rastrelliger faughni, and Rastrelliger  brachysoma. Genetic diversity varied among the five focal species analyzed; Thunnus albacares and Auxis thazard exhibited the lowest haplotype diversity, indicating potential population vulnerability. Intraspecific genetic distances were below 2%, while interspecific distances exceeded 2%, confirming the effectiveness of the COI gene for species discrimination. Phylogenetic reconstruction produced well-supported clades consistent with established taxonomic relationships. The observed species composition in Cenderawasih Bay was dominated by widespread Indo-Pacific taxa. Notably, among the five tuna species (Thunnus spp.) known to occur in Indonesian waters, only Thunnus albacares and Thunnus obesus was detected in Cenderawasih Bay, raising the question of what ecological and oceanographic factors limit the presence of other tuna species. The ecological characteristics of Cenderawasih Bay are suggested to contribute to shaping the local Scombridae diversity patterns. These findings provide a fundamental genetic reference for Scombridae fisheries management and highlight the need for further oceanographic and ecological studies to understand the mechanisms driving species composition in the unique marine environment of Cenderawasih Bay.
Co-Authors Abdul H.A. Toha Abdul Hamid A. Toha Aradea Bujana Kusuma Destia Fitri Ariyani Dwi Muhammad Maulana Emmanuel Manangkalangi Esie Mega Wangi Jeni Jeni Muhammad Dailami Muhammad Dailami Robi Binur Sipriyadi Sipriyadi Wahyu Endra Kusuma Yerri D Mundoni