COI-Based DNA Barcoding of Selais Fish from Arut River, Central Kalimantan, Indonesia

Tomi Kasayev(1), Tuty Arisuryanti(2*)

(1) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(2) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta 55281
(*) Corresponding Author


Selais fish belongs to the family Siluridae consisting of 12 genera with 104 properly validated species. The human need for these fish has sharply increased due to the benefits provided, especially for consumption. However, morphologically the selais fish are slightly challenging to differentiate among other silurid fish for non-specialist experts. Thus, a DNA barcoding approach using the mitochondrial COI gene as a molecular marker in this study was applied to clarify a taxonomic position and classification species of selais fish from Arut River (Central Kalimantan, Indonesia) and was also to assembly fish COI database storage from Indonesia. In this research, the method used was a PCR (Polymerase Chain Reaction) method with a pair of universal barcoding primers, FishF2 and FishR2. Based on partial COI fragment-based DNA barcoding, the whole samples showed no sequence differences (only 1 haplotype) within the population and this confirmed that these fish only consisted of one identical species. Furthermore, phylogenetic analysis (NJ / ML / BI) revealed that selais fish in this study had a close genetic relationship with Ompok hypophthalmus compared to other Ompok groups. This relationship was supported by the genetic distance value not exceeding 3.6% and this evaluated the undetermined naming of the selais fish from Arut River which was previously still unclassifiable.


Selais Fish, Siluridae, DNA Barcoding, COI gene, Phylogenetic

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Arisuryanti et al., 2018. Genetic identification of two mudskipper species (Pisces: Gobiidae) from Bogowonto Lagoon (Yogyakarta, Indonesia) using COI mitochondrial gene as a DNA barcoding marker. AIP Conference Proceedings, 2002. doi: 10.1063/1.5050164.

Arisuryanti et al., 2020a. Determination of species boundaries of Selais fish from Arut River, Central Kalimantan based on 16S mitochondrial gene using Bayesian approach. BIO Web of Conferences, 28. doi: 10.1051/bioconf/20202801003.

Arisuryanti et al., 2020b. Composition of mitochondrial DNA COI nucleotide of striped snakehead (Channa striata Bloch, 1793) collected from three rivers in Sumatra and Kalimantan. AIP Conference Proceedings, 2260. doi: 10.1063/5.0015907

Chang, C.H. et al, 2016. DNA barcode identification of fish products in Taiwan: Government-commissioned authentication cases. Food Control, 66, pp. 38-43. doi: 10.1016/j.foodcont.2016.01.034.

Chen, C. et al., 2021. DNA barcoding of yellow croakers (Larimichthys spp.) and morphologically similar fish species for authentication. Food Control, 127(4), p.108087. doi: 10.1016/j.foodcont.2021.108087

Cline, E., 2012. Marketplace substitution of Atlantic salmon for Pacific salmon in Washington State detected by DNA barcoding. Food Research International, 45(1), pp.388-393. doi: 10.1016/j.foodres.2011.10.043

Darriba, D. et al., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), pp.772-772. doi: 10.1038/nmeth.2106

Fricke, R., Eschmeyer, W. N. & Fong, J. D., 2021. ‘Eschmeyer's Catalog of Fishes: Genera/Species By Family/Subfamily’, viewed 10 May 2021, from

Hebert, P.D. et al., 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), pp.313-321. doi: 10.1098/rspb.2002.2218

Jusmaldi, N.F.N. et al., 2017. Kode batang DNA ikan lais genus Kryptopterus asal Sungai Mahakam, Kalimantan Timur [Barcoding DNA of catfish species genus Kryptopterus from Mahakam River, East Kalimantan]. Jurnal Iktiologi Indonesia, 14(3), pp.191-199. doi: 10.32491/jii.v14i3.80.

Jusmaldi, J. et al., 2018. Sebaran dan kekayaan spesies ikan lais (famili Siluridae) di Sungai Mahakam Kalimantan Timur [Distribution and species diversity of lais fish (family Siluridae) from Mahakam River, East Kalimantan]. Proceeding of Biology Education, 2(1), pp.18-25.

Kottelat, M., 2013. The fishes of the inland waters of Southeast Asia: a catalogue and core bibliography of the fishes known to occur in freshwaters, mangroves and estuaries. Raffles Bulletin of Zoology, 27, pp. 1-663

Kumar, S. et al., 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), p.1547-1549. doi:10.1093/molbev/msy096

Maddison, W. P. & Maddison, D.R., 2018, ‘Mesquite: a modular system for evolutionary analysis version 3.61’, viewed 10 February 2021, from

Malakar, A.K. et al., 2012. Molecular identification of three Ompok species using mitochondrial COI gene. Mitochondrial DNA, 23(1), pp.20-24. doi: 10.3109/19401736.2011.643876

Mitani, T. et al., 2009. Identification of animal species using the partial sequences in the mitochondrial 16S rRNA gene. Legal Medicine, 11, pp. S449-S450. doi: 10.1016/j.legalmed.2009.02.002.

Ng, H.H., 2003. A review of the Ompok hypophthalmus group of silurid catfishes with the description of a new species from South‐East Asia. Journal of Fish Biology, 62(6), pp.1296-1311. doi:10.1046/j.1095-8649.2003.00107

Pandey, P.K. et al., 2020. DNA barcoding and phylogenetics of freshwater fish fauna of Ranganadi River, Arunachal Pradesh. Gene, 754, p.144860. doi: 10.1016/j.gene.2020.144860.

Panprommin, D. et al., 2019. DNA barcodes for the identification of species diversity in fish from Kwan Phayao, Thailand. Journal of Asia-Pacific Biodiversity, 12(3), pp.382-389. doi: 10.1016/j.japb.2019.05.003.

Peakall, R. & Smouse, P.E., 2012, GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28(19), pp. 2537-2539. doi:10.1093/bioinformatics/bts460.

Rambaut, A., 2019, ‘FigTree v 1.4.4.’ viewed 10 February 2021, from

Roesma, D.I., Tjong, D.H. & Aidil, D.R., 2020. Phylogenetic analysis of transparent gobies in three Sumatran lakes, inferred from mitochondrial Cytochrome Oxidase I (COI) gene. Biodiversitas Journal of Biological Diversity, 21(1), pp.43-48. doi: 10.13057/biodiv/d210107.

Rozas, J. et al., 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34(12), pp.3299-3302. doi:10.1093/molbev/msx248.

Suchard, M.A. et al., 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4(1), p.vey016. doi: 10.1093/ve/vey016.

Ward, R.D. et al., 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), pp.1847-1857. doi: 10.1098/rstb.2005.1716.

Xu, L. et al., 2021. Assessment of fish diversity in the South China Sea using DNA taxonomy. Fisheries Research, 233, p.105771. doi: 10.1016/j.fishres.2020.105771.

Zemlak, T.S. et al., 2009. DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources, 9, pp.237-242. doi: 10.1111/j.1755-0998.2009.02649.x.


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