Comparison of CYB Gene Sequence for Species Identification of Tuna Fish

Beivy Jonathan Kolondam


DNA barcoding is a reliable tool for species identification, especially for authentication of processed fish products. In the process of authentication of tuna fish products, this tool is needed due to its small sample requirement for species identification. This research aimed to conduct an assessment for the use of the Cytochrome B (CYB) gene sequence for tuna fish identification through DNA barcoding. The same set of mitochondrial DNA genomes were used for the previous COI gene for in silico comparison of tuna fish species. Group comparison of the CYB gene between Bluefin tuna (five species), Yellowfin tuna (three species), and other groups of tuna (five species) showed that this gene is reliable to differentiate all of the specimens of each species. The result displayed by the multiple sequence alignment indicated enough resolution for accurate identification. The problem in the differentiation of Thunnus orientalis dan T. thynnus by the COI gene in the previous study was finally resolved by the CYB gene. From 1141 bp of nucleotides compared in all specimens, there were 248 differentiation sites. All of the members of Thunnus were differentiated for other genera (Auxis, Euthynnus, and Katsuwonus) in 40 differentiation sites. 

Keywords: DNA barcoding; CYB gene; tuna fish


DNA barcoding merupakan perangkat yang dapat diandalkan untuk identifikasi spesies ikan, terutama untuk kepentingan autentifikasi produk-produk olahan hasil perikanan. Dalam proses autentifikasi produk hasil olahan ikan tuna memerlukan metode ini karena hanya membutuhkan sampel yang sangat sedikit untuk identifikasi spesies. Penelitian ini bertujuan untuk melakukan asesmen terhadap penggunaan sekuens gen sitokrom B (CYB) untuk identifikasi ikan tuna lewat DNA barcoding. Genom DNA mitokondria yang sama dengan penelitian gen COI sebelumnya digunakan untuk perbandingan secara in silico spesies-spesies ikan tuna. Perbandingan sekuens gen CYB pada kelompok ikan tuna Bluefin (lima spesies), kelompok ikan tuna Yellowfin (tiga spesies), dan kelompok ikan tuna jenis lain (lima spesies) menunjukkan bahwa gen ini mampu membedakan semua spesies yang dibandingkan. Hasil yang digambarkan dari penjajaran sekuens menunjukkan resolusi yang cukup untuk identifikasi secara akurat. Spesies Thunnus orientalis dan T. thynnus yang memiliki variasi sekuens yang identik di gen COI berdasarkan penelitian sebelumnya ternyata bisa dibedakan melalui gen CYB ini. Dari 1.141 bp nukleotida yang dibandingkan, terdapat 248 titik perbedaan. Semua anggota dari genus Thunnus berbeda dengan spesimen dari genus-henus lainnya (Auxis, Euthynnus, dan Katsuwonus) di 40 titik nukleotida.

Kata kunci: DNA barcoding; gen CYB; ikan tuna


DNA barcoding; CYB gene; tuna fish

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Aranishi, F., T. Okimoto, dan S. Izumi. (2005) Identification of Gadoid Species (Pisces, Gadidae) by PCR-RFLP Analysis. Journal of Applied Genetics 46(1): 69–73.

Bottero, M. T., A. Dalmasso, M. Cappelletti, C. Secchi, dan T. Civera (2007) Differentiation of Five Tuna Species by a Multiplex Primer-extension Assay. JOURNAL OF BIOTECHNOLOGY, 129(3), 575–580.

Catanese, G., C. Infante, dan M. Manchado (2008) Complete Mitochondrial DNA Sequences of the Frigate Tuna Auxis thazard and the Bullet Tuna Auxis rochei. DNA SEQUENCE,19(3), 159-166.

Chen, C., Y. Li, H. Yu, S. Peng, S. Sun, L. Wang, X. Meng, Y. Huang dan X. Kong (2014) Thunnus orientalis Mitochondrion, Complete Genome [diakses 27 Februari 2020]

Dooley, J.J., H.D. Sage, M.L. Clarke, H.M. Brown, dan S.D. Garrett (2005) Fish Species Identification using PCR−RFLP Analysis and Lab-on-a-Chip Capillary Electrophoresis: Application to Detect White Fish Species in Food Products and an Interlaboratory Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 53(9), 3348-3357.

Dudu, A., T. Barbălată, G. Popa, S. Georgescu, dan M. Costache (2016) Advantages and Limitations of DNA Barcoding in Identifying Commercially-Exploited Fish Species. SCIENTIFIC PAPERS ANIMAL SCIENCE AND BIOTECHNOLOGIES, 49(1), 45-49.

Edgar, R.C. (2004) MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput. NUCLEIC ACIDS RESEARCH, 32(5), 1792-1797.

Hebert, P.D., A. Cywinska, S.L. Ball dan J.R. de Waard (2003) Biological Identifications through DNA Barcodes. PROCEEDINGS OF ROYAL SOCIETY B BIOLOGICAL SCIENCES, 270(1512), 313–321.

Hellberg, R.S.R., dan M.T. Morrissey (2011) Advances in DNA-Based Techniques for the Detection of Seafood Species Substitution on the Commercial Market. JALA: JOURNAL OF THE ASSOCIATION FOR LABORATORY AUTOMATION, 16(4), 308-321.

Infante, C., G. Catanese dan M. Manchado (2006) Euthynnus alletteratus Mitochondrion, Complete Genome. [diakses 27 Februari 2020]

Kearse, M., R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, C. Duran, T. Thierer, B. Ashton, P. Meintjes, and A. Drummond (2012) Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data. BIOINFORMATICS, 28(12), 1647-1649.

Kolondam, B.J. (2020) Variasi Sekuens Gen COI untuk DNA Barcoding Ikan Tuna. MEDIA TEKNOLOGI HASIL PERIKANAN, 8(2), 70-75.

Li, M., L. Guo, H. Zhang, S. Yang, X. Chen, Z. Meng, dan H. Lin (2014a). Auxis rochei Mitochondrion, Complete Genome. [diakses 27 Februari 2020]

Li, M., L. Guo, H. Zhang, S. Yang, X. Chen, Z. Meng dan H. Lin (2014b) Euthynnus affinis Mitochondrion, Complete Genome. [diakses 27 Februari 2020].

Li, Y., C. Chen, H. Yu, S. Peng, S. Sun, L. Wang, X. Meng, Y. Huang dan X. Kong (2016) The Complete Mitochondrial Genome of the Southern Bluefin tuna Thunnus maccoyii. MITOCHONDRIAL DNA, 27(6), 3921-3922.

Manchado, M., G. Catanese, A. Crespo dan C. Infante (2016) Thunnus alalunga Mitochondrial DNA, Complete Genome. [diakses 27 Februari 2020].

Márquez, E.J., J.P. Isaza and J.F. Alzate (2016) Mitochondrial Genome of the Blackfin Tuna Thunnus atlanticus Lesson, 1831 (Perciformes, Scrombidae), MITOCHONDRIAL DNA, 27(3), 1771-1772.

Martinez-Ibarra, C., S. Ishizaki dan Y. Nagashima (2016a) Thunnus obesus Mitochondrion, Complete Genome. [diakses 27 Februari 2020].

Martinez-Ibarra, C., S. Ishizaki dan Y. Nagashima (2016b) Katsuwonus pelamis Voucher KP02-2318 Mitochondrion, Complete Genome. [diakses 27 Februari 2020].

Martinez-Ibarra, C., S. Ishizaki dan Y. Nagashima (2013) Thunnus tonggol Mitochondrion, Complete Genome. [diakses 27 Februari 2020].

Martinez-Ibarra, C., S. Ishizaki, S. dan Y. Nagashima (2010) Thunnus albacares Mitochondrion, Complete Genome. [diakses 27 Februari 2020].

Nurilmala, M., U. Widyastuti, W.A. Kusuma, Nurjanah, N. Wulansari, Y. Widyatuti. 2016. DNA Barcoding for Identification of Processed Tuna Fish in Indonesian Market. JURNAL TEKNOLOGI, 78(4), 115–118

Rasmussen, R.S., dan Morrissey, M.T. 2008. DNA-based Methods for the Identification of Commercial Fish and Seafood Species. COMPREHENSIVE REVIEW OF FOOD SCIENCE AND FOOD SAFETY, 7(3), 280-295.

Satoh, T.P., M. Miya, K. Mabuchi dan M. Nishida (2016) Structure and Variation of the Mitochondrial Genome of Fishes. BMC GENOMICS, 17(1), 719.

Wulansari, N., M. Nurilmala dan Nurjanah (2015) Deteksi Ikan Tuna dan Produk Olahannya Berbasis Protein dan DNA Barcoding. JURNAL PENGOLAHAN HASIL PERIKANAN INDONESIA, 18(2), 119-127.

Xiong, X., F. Yuan, M. Huang, L. Lu, X. Xiong, J. Wen (2019) DNA Barcoding Revealed Mislabeling and Potential Health Concerns with Roasted Fish Products Sold across China. JOURNAL OF FOOD PROTECTION, 82 (7), 1200-1209.



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