Composition of Mitochondrial DNA 16S Nucleotide of Dwarf Snakehead (Channa gachua Hamilton, 1822) from Keji River, Magelang, Central Java

https://doi.org/10.22146/jtbb.35613

Warisatul Ilmi(1), Tuty Arisuryanti(2*)

(1) Universitas Gadjah Mada
(2) Universitas Gadjah Mada
(*) Corresponding Author

Abstract


Indonesia has a high marine and freshwater biodiversity including freshwater fish biodiversity. One of freshwater fish which is commonly consumed by Indonesian people is dwarf snakehead (Channa gachua Hamilton, 1822). However, research on genetic characterization, especially the composition of mtDNA 16S nucleotide of dwarf snakehead has poorly understood. Therefore, the aim of this study was to determine the composition of mtDNA 16S nucleotide of dwarf snakehead as a part of genetic characterization of the fish species taken from Keji River, Magelang, Central Java which has not been previously examined. This study analyzed 16S mt-DNA of two samples of dwarf snakehead from Keji River (KTS-01 and KTS-02). In addition, two sequences of Channa gachua with accession number KU986900, KU238074, and HM117234-HM117238 taken from GenBank were used as a comparison. A method used in this research was a PCR method and primers used in this research were 16Sar and 16Sbr. The results revealed that the average of nucleotide composition T, C, A and G of the fish species was 23.04%, 25.13%, 29.06% and 22.77% respectively whereas the average rate of nucleotide composition A+ T and G+ C was 52.10% and 47.90% respectively. The two dwarf snakehead had similar T and C composition but different in A and G composition. In addition, the G+C content in KTS-01 and KTS-02 had the highest frequency compared to other dwarf snakehead taken from GenBank. From this finding it could be assumed that there is genetic variation between the two dwarf snakehead from Keji River which is important genetic data for breeding program of the fish species in the future.


Keywords


dwarf snakehead; genetic characterization; mtDNA 16S; nucleotide composition

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References

Arif, I.A., Khan, H.A., Bahkali, A.H., Al Homaidan, A.A., Al Farhan, A.H., Shobrak, M. & Al Sadoon, M., 2009, Comparison of neighbor-joining and maximum parsimony methods for molecular phylogeny of Oryx species using 12S rRNA and 16S rRNA gene sequences, Animal Biology Journal, 1(2), 117-125.

Arif, I.A. & Khan, H.A., 2009, Molecular markers for biodiversity analysis of wildlife animals: a brief review, Animal Biodiversity and Conservation, 32(1), 9–17.

Arisuryanti, T., 2016, Molecular Genetic and Taxonomic Studies of the Swamp Eel (Monopterus albus Zuiew 1793). Ph.D. Thesis, Charles Darwin University, Australia.

Benziger A., Philip, S., Raghavan, R., Ali, P.H.A., Sukumaran8, M., Tharian, J.S., Dahanukar, N., Baby, F., Peter, R., Devi, K.R., Radhakrishnan, K.V., Haniffa, M.A., Britz, R. & Antunes, A., 2011, Unraveling a 146 years old taxonomic puzzle: Validation of Malabar snakehead, species-status and its relevance for Channid systematics and evolution, Validation of Malabar Snakehead Species-Status, 6(6), 1-12.

Berra, T.M., 2007, Freshwater Fish Distribution, The University of Chicago Press, Chicago.

Chaundhry, S., 2010, ‘Channa gachua’, in The IUCN Red List of Threatened Species 2010, viewed 05 January 2018, from http://www.iucnredlist.org/details/166123/0.

Cheng, Q., Ma, C., Cheng, H. & Zhang, Q., 2008, Mitochondrial DNA diversity of Coilia mystus (Clupeiformes: Engraulidae) in three Chinese estuaries, Environmental Biology of Fishes, 83(3), 277-282.

Cheng, S.S., Senoo, S., Siddiquee, S. & Rodrigues, K.F. 2015. Genetic variation in the mitochondrial genome of the giant grouper Epinephelus lanceolatus (Bloch, 1790) and its application for the identification of brood stock, Aquaculture Reports, 2, 139-143.

Hammer, M.P., Unmack, P.J. & Adams, M., 2014, A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia, Biological Journal of the Linnean Society, 111, 521-540.

Jahan, H., Akter, M., Begum, R.A. & Shahjahan, R.M., 2017, Identification and comparison of three carp fishes based on mitochondrial 16S rRNA gene. Journal Biological Science, 26(2), 167-174.

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, 27, 1-663.

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(6), 1212-1219.

Librado, P. & Rozas, J., 2009, DnaSP v5: A Software for Comprehensive Analysis of DNA Polymorphism Data, Bioinformatics, 25, 1451-1452.

Milton, J., Bhat, A.A., Haniffa, M.A., Hussain, S.A., Rather, I.A., Al-Anazi, K.M., Hailan, W.A.Q. & Farah, M.A., 2017, Ovarian development and histological observations of threatened dwarf snakehead fish, Channa gachua (Hamilton, 1822), Saudi Journal of Biological Sciences, 1(25), 149-153.

Palumbi, S.R., 1996, ‘Nucleid acids II : The Polymerase Chain Reaction’, in D.M. Hillis, C. Moritz, B.K. Mable (eds.), Molecular Systematic, pp. 205-247, Sinauer Associates, Massachusetts.

Pereira, F., Carneiro, J. & Amorim, A., 2008, Identification of species with DNA-Based Technology: Current progress and challenges. Recent Patents on DNA and Gene Sequences, 2, 187-200.

Satoh, T.P., Miya, M., Mabuchi, K. & Nishida, M., 2016, Structure and variation of the mitochondrial genome of fishes. Biomed Central Genomics, 17(719), 1-20.

Yang, L., Tan, Z., Wang, D., Xue, L., Guan, M., Huang, T. & Li, R., 2014, Species identification through mitochondrial rRNA genetic analysis. Scientific Reports, 4, 4089.



DOI: https://doi.org/10.22146/jtbb.35613

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