Molecular Characterization of Danau Selais Fish (Ompok hypophthalmus) and Kaporeh Selais Fish (Ompok eugeneiatus) from Riau Province of Indonesia using Mitochondrial 12S rRNA
DOI:
10.29303/jbt.v23i1.5709Published:
2023-11-02Downloads
Abstract
The floodplain river in Riau is inhabited by various types of vertebrate animals including fish from the genus Ompok. The rapid development of species in the Ompok genus can cause ambiguity in species identity due to inaccurate identification processes. This research aims to analyze the molecular characteristics of two types of selais fish, namely danau selais fish (O. hypophthalmus) and kaporeh selais fish (O. eugeneiatus) from Riau based on 12S rRNA sequences. Methods included sampling of fishes from the Kampar, Tapung and Indragiri Rivers, the total DNA isolation, PCR, electrophoresis, sequencing and data analysis. In this study, the 12S rRNA DNA sequence of the selais fish studied was 939 bp in size. The sequences consisted of 803 bp of conserved sites (86.15%), 127 bp of variable sites (13.52%), 53 bp of parsimony sites (5.64%) and 73 bp of singleton sites (18.57%), with the composition of Adenine 31.7 %, Cytosine 26.9%, Thymine 20.9% and Guanine 20.4%. The average genetic distance between the two species was ±0.034, with the lowest genetic distance identified in the species O. hypophthalmus and O. eugeneiatus from the Indragiri River with a value of ±0.032, while the farthest genetic distance was identified in the species O. eugeneiatus from the Kampar River and the species C. gariepinus (Out group) with a value of ±0.092. Transition substitution (19.50%) occurs more frequently than transversion (10.94%). Phylogenetic reconstruction showed that the two species can be separated into distinct groups based on 12S rRNA sequences.
Keywords:
12S rRNA, floodplain, Ompok sp., Riau, selais fish.References
Baştanlar, E. K. (2019). Identification of Mislabelling in Frozen Fish Fillets Based on DNA Barcoding Analysis. Marine Science and Technology Bulletin, 8(1): 30–35.
Bingpeng, X., Heshan, L., Zhilan, Z., Chunguang, W., & Yanguo, W. (2018). DNA barcoding for identification of fish: species in the Taiwan Strait. PloS ONE, 13(16): e0198109.
Cawthorn D. M., Steinman H. A., & Witthuhn R. C. (2012). Evalution of 16S and 12S Rrna genes as universal markers for the identification of commercial fish species in South Africa. Gene, 491(1): 40-48.
Cawthorn, D. M., Baillie, C., & Mariani, S. (2018). Generic names and mislabeling conceal high species diversity inglobal fisheries markets. Conservation Letters, 11:e12573.
Chan, A. H. E., Saralamba, N., Saralamba, S., Ruangsittichai, J., & Thaenkham, U. (2022). The potential use of mitochondrial ribosomal genes (12S and 16S) in DNA barcoding and phylogenetic analysis of trematodes. BMC Genomics, 23: 104. https://doi.org/10.1186/s12864-022-08302-4.
De Alwis, P. S., Kundu, S., Gietbong, F. Z., Amin, M. H. F., Lee, S.-R., Kim, H.-W., & Kim, A. R. (2023). Mitochondriomics of Clarias fishes (Siluriformes: Clariidae) with a new assembly of Clarias camerunensis: Insights into the genetic characterization and diversification. Life, 13(2): 482-500.
Elvyra, R. & Roslim, D.I. (2016). Keanekaragaman Genetik dan Barkode DNA Ikan Selais di Provinsi Riau. Pekanbaru: UR Press.
Elvyra, R. (2023). The DNA barcode of cytb on selais bungkuk fish (Hemisilurus heterorhynchus Bleeker) originating from Riau, Indonesia. Jurnal Biologi Tropis, 23(3): 429-435.
Elvyra, R., Nurasiah, N., & Batubara, A. S. (2023). Molecular characterization of Tapah fish (Wallago leerii, Bleeker 1851) from Riau Province based on Cytochrome b gen. Depik: Jurnal Ilmu-ilmu Perairan, Pesisir dan Perikanan, 12(2): 243-349.
Fukunaga, N., Shimizu, M., Teruya, S., Razali, N. N., Nakashima, S., Tomobuchi, N., Sasaki, T., & Setiamarga, D. H. E. (2021). Reassessment of the mitochondrial 12S-rRNA gene for DNA barcoding of museum specimens of shelled marine gastropods from Japan. E3S Web of Conferences, 322: 01028.
Hu, Z., Wang, Z., Zhang, S., Biang, Y., & Li, C. (2015). Species identification through pyrosequencing 12S rRNA gene. Forensic Science International: Genetics Supplement Series, 5: e561-e563.
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: 1-663.
Lemoine, F., Entfellner, J.-B. D., Wilkinson, E., Correia, D., Felipe, M. D., De Oliveira, D., & Gascuel, O. (2018). Nature, 556(7702): 452-456.
Liu, S., Shen, S., Wu, P., Li, F., Liu, X., Wang, C., Gong, Q., Wu, J., Yao, X., Zhang, H., & Shi, Y. (2019). Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function. Nucleic Acids Research, 47(14): 7648-7665.
Milan, D. T., Mendes, I. S., Damasceno, J. S., Teixeira, D. F., Sales, N. G., & Carvalho, D. C. (2020). New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment. Scientific Reports, 10: 17966.
Munguia-Vega, A., Weaver, A. H., Domínguez-Contreras, J. F., & Peckham, H. (2022) Multiple drivers behind mislabeling of fish from artisanal fisheries in La Paz, Mexico. PLoS ONE, 17(4): e0265960.
Panicker, V. P., Haridas, P. C., Narayanan, A., Mohammed, S., & Babu, B. C. (2019). Mitochondrial 12S rRNA gene sequence analysis, a tool for species identification. Journal of Wildlife and Biodiversity, 3(3): 29-35.
Prakrongrak, N., Boongsoong, B., & Monthatong, M. (2023). Genetic diversity and phylogenetic analysis of mayfly Caenis (Insecta: Ephemeroptera) using Cytochrome C Oxidase I (COI) and 12s rRNA genes from Thailand. Biodiversitas, 24(4): 1990-1998.
Putra, A., Wisha, U. J., & Kusumah, G. (2017). Spatial analysis of the river line and land cover changes in the Kampar Rivers estuary: The influence of the bono tidal bore phenomenon. Indonesian Journal of spatial and region analysis, 31(2): 220-231.
Riduan, R. (2019). Karakterisasi Molekuler Ikan Ompok hypophthalmus (Blekker 1846) asal Sungai Kampar Provinsi Riau dengan Menggunakan Penanda 12S rRNA. [skripsi]. Pekanbaru: Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Riau.
Rosenberg, N. A., Li, L. M., Ward, R., & Pritchard, J. K. (2003). Informativeness of genetic markers for inference of ancestry. American Journal of Human Genetic. 73(6):1402-1422.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis Version 6.0. Molecular Biology and Evolution, 30: 2725-2729.
Wang H. Y. & Lee S. C. (2002). Secondary stucture of mithocondrial 12S rRNA among fish and its phylogenetic applications. Molecular Biology and Evolution, 19(2): 138-148.
Yang, L., Tan, Z., Wang, D., Xue, L., Guan, M., Huang, T., & Li, R. (2014). Species identification through mitochondrial Rrna genetic analysis. Science reports, 4: 4089.
Zhang, R., Zhu, T., & Luo, Q. (2023). The complete mitochondrial genome of the freshwater fish Onychostoma ovale (Cypriniformes, Cyprinidae): genome characterization and phylogenetic analysis. Genes. 14(6): 1227-1238.
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