Genetic Characterization of Caesio cuning (Bloch, 1791) Using COI Gene Markers in the Marine Waters of North Maluku and North Sulawesi
DOI:
https://doi.org/10.35800/jip.v13i2.61579Keywords:
Caesio cuning, COI gene, DNA barcoding, genetic structure, phylogenetic analysisAbstract
This research investigates the genetic composition of C. cuning (Bloch, 1791) inhabiting the coastal waters of North Maluku and North Sulawesi through the application of DNA barcoding, utilizing the mitochondrial COI (Cytochrome c Oxidase subunit I) gene as a molecular marker. Specimens were obtained from four distinct sampling sites: Ternate, Guraping, Ratatotok, and Manado. DNA was extracted using a commercially available kit, followed by amplification via PCR and sequence analysis using the MEGA X platform. Sequencing results produced a 611 bp fragment of the COI gene, with a nucleotide profile dominated by pyrimidine bases—specifically thymine and cytosine. Genetic similarity between local samples and GenBank references ranged from 99.08% to 100%, indicating a high level of genetic uniformity. Phylogenetic reconstruction showed that populations from the four locations clustered with C. cuning populations from other western Indo-Pacific regions, including East Java, Bali, and the Philippines. These findings support the recognition of C. cuning in the study area as a single, genetically cohesive stock suitable for regionally coordinated conservation and sustainable fishery management.
Keywords: C. cuning, COI gene, DNA barcoding, genetic structure, phylogenetic analysis.
Abstrak
Penelitian ini mengkaji komposisi genetik ikan C. cuning (Bloch, 1791) yang tertangkap erairan pesisir Maluku Utara dan Sulawesi Utara melalui pendekatan DNA barcoding dengan menggunakan gen mitokondria COI (Cytochrome c Oxidase subunit I) sebagai penanda molekuler. Spesimen dikumpulkan dari empat lokasi sampling yang berbeda, yaitu Ternate, Guraping, Ratatotok, dan Manado. Ekstraksi DNA dilakukan menggunakan kit komersial, dilanjutkan dengan amplifikasi melalui PCR serta analisis sekuens menggunakan perangkat lunak MEGA X. Hasil sekuensing menghasilkan fragmen gen COI sepanjang 611 bp, dengan komposisi nukleotida yang didominasi oleh basa pirimidin—khususnya timin dan sitosin. Tingkat kemiripan genetik antara sampel lokal dan referensi dari GenBank berkisar antara 99,08% hingga 100%, menunjukkan tingkat homogenitas genetik yang tinggi. Rekonstruksi filogenetik memperlihatkan bahwa populasi dari keempat lokasi tergabung dalam satu klade dengan populasi C. cuning dari wilayah lain di Indo-Pasifik bagian barat, termasuk Jawa Timur, Bali, dan Filipina. Temuan ini mendukung pengakuan bahwa C. cuning di wilayah studi merupakan satu stok genetik yang kohesif dan sesuai untuk dikelola secara kolektif dalam upaya konservasi serta pengelolaan perikanan berkelanjutan di tingkat regional.
Kata kunci: C. cuning, gen COI, DNA barcoding, struktur genetik, analisis filogenetik
References
Ackiss, A. S., Bird, C. E., Akita, Y., Santos, M. D., Tachihara, K., & Carpenter, K. E. (2018). Genetic patterns in peripheral marine populations of the fusilier fish C. cuning within the Kuroshio Current. Ecology and Evolution, 8(23), 11875–11886. https://doi.org/10.1002/ece3.4644
Brown, W. M., George, M., & Wilson, A. C. (1979). Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences, 76(4), 1967–1971. https://doi.org/10.1073/pnas.76.4.1967
Fricke, R., Kulbicki, M., & Wantiez, L. (2011). Checklist of the fishes of New Caledonia, and their distribution in the Southwest Pacific Ocean (Pisces). Stuttgarter Beiträge zur Naturkunde A, Neue Serie, 4, 341–463.
Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H., & Hallwachs, W. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences, 101(41), 14812–14817. https://doi.org/10.1073/pnas.0406166101
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111–120. https://doi.org/10.1007/BF01731581
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
Lanave, C., Preparata, G., Saccone, C., & Serio, G. (1984). A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution, 20(1), 86–93. https://doi.org/10.1007/BF02101990
Mabuchi, K., Fraser, T. H., Song, H., Azuma, Y., & Nishida, M. (2014). Revision of the systematics of the cardinal fishes (Percomorpha: Apogonidae) based on molecular analyses and comparative reevaluation of morphological characters. Zootaxa, 3846(2), 151–203. https://doi.org/10.11646/zootaxa.3846.2.1
Nursalim, N., Trianto, A., Cahyani, N. K. D., Kholilah, N., Janarkho, G. F., & Hardianto, E. (2022). Genetic and Morphological Variation of the Redbelly Yellow Tail Fusilier, C. cuning (Bloch, 1971) from the Nyamuk Waters, Karimunjawa Archipelago. 27.
Peng, Z., He, S., & Zhang, Y. (2004). Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences. Molecular Phylogenetics and Evolution, 31(3), 979–987. https://doi.org/10.1016/j.ympev.2003.10.023
Rembet, U. N., Boer, M., Bengen, D. G., & Fahrudin, A. (2011). Struktur Komunitas Ikan Target Di Terumbu Karang Pulau Hogow Dan Putus-Putus Sulawesi Utara. Jurnal Perikanan Dan Kelautan Tropis, 7(2), 60. https://doi.org/10.35800/jpkt.7.2.2011.179
Rondonuwu, A. B., Lumingas, L. J. L., Bataragoa, N. E., Pratasik, S. B., Tilaar, F. F., & Salaki, M. S. (2020). Mitochondrial CO1 sequences of Banggai cardinal fish (BCF) from Lembeh Strait, North Sulawesi, Indonesia. AACL Bioflux, 13(2), 760–767.
Steinke, D., Zemlak, T. S., & Hebert, P. D. N. (2009). Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS ONE, 4(7), e6300. https://doi.org/10.1371/journal.pone.0006300
Vagelli, A. A. (2011). The Banggai cardinal fish: Natural history, conservation, and culture of Pterapogon kauderni. Wiley-Blackwell.
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1847–1857. https://doi.org/10.1098/rstb.2005.1716
Zhan, W., Chen, R., Shen, K., Xu, D., Hsiao, C. D., & Lou, B. (2017). Next-generation sequencing yields the complete mitochondrial genome of the redbelly yellowtail fusilier, C. cuning (Teleostei: Caesionidae). Mitochondrial DNA Part A, 28(1), 125–126. https://doi.org/10.3109/19401736.2015.1111353
Zuhdi, M. F., & Madduppa, H. (2020). Identifikasi C. cuning berdasarkan karakterisasi morfometrik dan DNA barcoding yang didaratkan di Pasar Ikan Muara Baru, Jakarta. Jurnal Kelautan Tropis, 23(2), 199–206. https://doi.org/10.14710/jkt.v23i2.7036
Downloads
Published
How to Cite
License
Copyright (c) 2025 Muh. Rafil Afdalul Firkan Marsaoly, Ari Berty Rondonuwu, Rosita Anggreiny. J Lintang, Stenly Wullur, Jety Kornela Rangan, Suzanne Lydia Undap
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
COPYRIGHT
Authors who publish with this journal agree to the following terms:
Authors hold their copyright and grant this journal the privilege of first publication, with the work simultaneously licensed under a Creative Commons Attribution License that permits others to impart the work with an acknowledgment of the work's origin and initial publication by this journal.
Authors can enter into separate or additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (for example, post it to an institutional repository or publish it in a book), with an acknowledgment of its underlying publication in this journal.
Authors are permitted and encouraged to post their work online (for example, in institutional repositories or on their website) as it can lead to productive exchanges, as well as earlier and greater citation of the published work (See The Effect of Open Access).
