GENETIC CHARACTERIZATION OF DWARF SNAKEHEAD, Channa gachua (Hamilton, 1822), FROM TWO POPULATIONS BASED ON 16S rRNA GENE
Abstract
Indonesia is one of the countries with high biodiversity of freshwater fishes. One freshwater fish with a wide distribution in Asia with high economic potency for ornamental fish is dwarf snakehead. However, research on genetic characterization of dwarf snakehead from Indonesia is very limited. Therefore, this research aimed to compare genetic characterization of the dwarf snakehead from rice field irrigation at Donomulyo Village (Malang, East Java) and from Keji River (Magelang, Central Java). This study used a PCR method with universal primers: 16Sar and 16Sbr. The data obtained in this study were then analyzed using DNASTAR, BLAST, Mesquite, MEGA, DnaSP, and NETWORK. The results revealed the genetic distance between dwarf snakehead from rice field irrigation at Donomulyo Village and from Keji River was 1.36%. The divergence of GC content, haplotype number, variables sites, haplotype diversity, and nucleotide diversity in both populations exist. The results of this study are expected to arrange 16S mitochondrial DNA Library of dwarf snakehead from Indonesia which is useful for a reference in the conservation and utilization and management of dwarf snakehead in their habitat.
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Ab Wahab, S.Z., Kadir, A.A., Hussain, N.H.N., Omar, J., Yunus, R., Baie, S., Mohd Noor, N., Hassan, I.I., Wan Mamood, W.H., Abd Razak, A., & Wan Yusoff, W.Z. (2015). The effect of Channa striatus (Haruan) extract on pain and wound he aling of post-lower segment c esarean section women. Hindawi, 2015, ID 849647.
Arisuryanti, T., Firdaus, N.U.N., & Hakim, L. (2020). Genetic characterization of striped snakehead (Channa striata Bloch, 1793) from Arut River, Central Kalimantan inferred from COI mitochondrial gene. AIP Conference Proceedings, 2260, 020001. https://doi.org/10.1063/5.0015905
Ahmed, M.S., Dina, S.R., Nahar, L., Islam, N.N., & Al Reza, H. (2018). Molecular characterization of Channa species from Bangladesh based on Cytochrome c Oxidase Subunit I (COI) gene. FishTaxa, 3(4), 87-93.
Cawthorn, D.M., Steinman, H.A., & Witthuhn, R.C. (2012). Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa. Gene, 491 (1), 40-48. DOI: 10.1016/j.gene.2011.09.009
Conte-Grand, C., Britz, R., Dahanukar, N., Raghavan, R., Pethiyagoda, R., Tan, H.H., Hadiaty, R.K., Yaakob, N.S., & Ruber, L. (2017). Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions. PLoSONE, 12(9), e0184017. https://doi.org/10.1371/journal.pone.0184017
Faddagh, M.S., Husain, N.A., & Al-Badran, A.I. (2012). Usage mitochondrial 16S rRNA gene as molecular marker in taxonomy of Cyprini fish species (Cyprinidae: Teleostei). Journal of King Abdulaziz University-Marine Sciences, (23)1, 39-49.
Hall, R. (2002). Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions, model and animations. Journal of Asian Earth Sciences, 20, 353-431. https://doi.org/10.1016/S1367-9120(01)00069-4
Hall, R. (2012). Sundaland and Wallacea: Geology, Plate Tectonics and Palaeogeography. in: Biotic Evolution and Environmental Change in Southeast Asia, (Eds.) D.J. Gower, J.E. Richardson, B.R. Rosen, L. Rüber, S.T. Williams, Cambridge University Press. UK, pp. 32-78
Gustiano R., Kurniawan K., & Kusmini, I.I. (2021). Bioresources and diversity of snakehead, Channa striata (Bloch 1793): a proposed model for optimal and sustainable utilization of freshwater fish. IOP Conf. Series: Earth and Environmental Science, 762 (012012), 1-13. doi:10.1088/1755-1315/762/1/012012
Hariati, A.M., Yuniarti, A., Endariani., Kusuma, W.E., & Wiadnya, D.G.R. (2019). Albumin and enzyme profiles of dwarf snakehead, Channa gachua caught from River Brantas, East Java. Journal of Physics: Conference Series, 1146, 012041. 10.1088/1742-6596/1146/1/012041
Hossain, M.A.M., Uddin, S.M.K., Chowdhury, Z.Z., Sultana, S., Johan, M.R., Rohman, A., Erwanto, Y., & Ali, M.E. (2019). Universal mitochondrial 16S rRNA biomarker for mini-barcode to identify fish species in Malaysian fish products. Food Additives & Contaminants Part A, 36(4), 493-506. DOI: 10.1080/19440049.2019.1580389
Ilmi, W., & Arisuryanti, T. (2018). Composition of Mitochondrial DNA 16S Nucleotide of Dwarf Snakehead (Channa gachua Hamilton, 1822) from Keji River, Magelang, Central Java. Journal of Tropical Biodiversity and Biotechnology, 3, 57-61. https://doi.org/10.22146/jtbb.35613
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. The Raffles Bulletin of Zoology, 2013 (Suppl. 27), 1-663.
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, 1547-1549. DOI: 10.1093/molbev/msy096
Lakra, W.S., Goswami, M., Gopalakrishnan, A., Singh, D.P., Singh, A., & Nagpure, N.S. (2010). Genetic relatedness among fish species of Genus Channa using mitochondrial DNA genes. Biochemical Systematics and Ecology, 38, 1212-1219. doi:10.1016/j.bse.2010.12.012
Maddison, W. P., & D.R. Maddison. (2019). Mesquite: a modular system for evolutionary analysis. Version 3.61 (http://www.mesquiteproject.org accessed 2 March 2020).
Palumbi, S.R. (1996). Nucleid acids II: The Polymerase Chain Reaction. in: Molecular Systematic, (Eds.) D.M. Hillis, C. Moritz, B.K. Mable, Sinauer Associates. Sunderland. Massachusetts, pp. 205-247.
Pinsky, M.L., & Palumbi, S.R. (2014). Meta-analysis reveals lower genetic diversity in overfished populations. Molecular Ecology, 23, 29–39
Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., & Sánchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large datasets. Molecular Biology and Evolution, 34, 3299-3302. DOI: 10.1093/molbev/msx248
Saad, Y.M., Shaikh Omar, A.K.M., & Gharbawi, W.M. (2019). Evaluation of molecular diversity in some Red sea parrotfish species based on mitochondrial 16S ribosomal RNA gene sequence variations. Research Journal of Biotechnology, 14(12), 8-21.
Satoh, T.P., Miya, M., Mabuchi, K., & Nishida, M. (2016). Structure and variation of the mitochondrial genome of fishes. BMC Genomics, 17, 719.
Srinivasan, R., Karaoz, U., Volegova, M., MacKichan, J., Kato-Maeda, M., Miller, S., Nadarajan, R., Brodie, E.L., Lynch, S.V. (2015). Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS ONE, 10(2), e0117617.
Tanomtong, A., Supiwong, W., Jearranaiprepame, P., Khakhong, S., Kongphironchuen, C., Getlekha, N. (2014). A new natural autotetraploid and chromosomal characteristics of dwarf snakehead fish, Channa gachua (Perciformes, Channidae) in Thailand. Cytologia, 79(1), 15-27.
Voris, H.K. 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. Journal of Biogeography, 27, 1153-1167.
Yang, L., T. Zongqing, D. Wang, L. Xue, M. Guan, T. Huang & R. Li. (2014). Species identification through mitochondrial rRNA genetic analysis. Science Report, 14, 1-11
Zhou, J., Deng, Y., Zhou, G. (2019). The mitochondrial genome of dwarf snakehead Channa gachua (Perciformes: Channidae) and phylogenetic analysis. Mitochondrial DNA Part B, 4(1), 1146-1147.
DOI: http://dx.doi.org/10.15578/ifrj.27.2.2021.109-116
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