DNA Authentication of Indonesian Leaffish Pristolepis grooti from Kelekar River and Ogan River in South Sumatra Based on Cytochrome C Oxidase Subunit I (COI) Gene

https://doi.org/10.22146/jtbb.74133

Mochamad Syaifudin(1*)

(1) Sriwijaya University
(*) Corresponding Author

Abstract


Indonesian leaffish Pristolepis grooti, an endemic species, are distributed in the region of Sumatra, Riau, Bangka Belitung and Kalimantan. However, there has been a decline in the population recently. This research purposed to investigate the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene, the genetic distance, the genetic tree of the leaffish and characterize the chemical physics of water of its habitat in the Kelekar River Muara Enim Regency and the Ogan River, Ogan Ilir Regency. The method used in species authentication was DNA isolation, amplification using PCR (Polymerase Chain Reaction) and sequencing of COI gene. The size of the COI mtDNA gene fragment was 704 bp (PM 1, PM 4, PP 2 and PP 4) and 723 bp (PM 2, PM 3, PP 1 and PP 3). A cryptic diversity of the species P. grooti is found based on the genetic distance value of 4.5-6%, both in the Kelakar and Ogan Rivers. The phylogenetic tree of the leaffish of this study formed 2 separate sub-clusters with a bootstrap value of 50%. The properties of water qualities in the two rivers included temperatures 28.3-31.8°C, pH 5.6-8.3, dissolved oxygen 4.82-10.89 mg L-1, alkalinity 10-28 mg L-1 CaCO3, water transparency 16-45 cm, ammonia 0.47-0.70 mg L-1, water current 0.17-0.30 m s-1 and TDS 7-44 mg L-1.

 


Keywords


cytochrome c oxidase subunit I (COI) gene, Kelekar River, leaffish, Ogan River, phylogenetics

Full Text:

PDF


References

Bączkiewicz, A. et al., 2017. DNA barcoding, ecology and geography of the cryptic species of Aneura pinguis and their relationships with Aneura maxima and Aneura mirabilis (Metzgeriales, Marchantiophyta). PLoS ONE, 12(12). doi: 10.1371/journal.pone.0188837.

Bühler, D. et al., 2014. Genetic damage induced by water pollutants in the freshwater fish Hyphessobrycon luetkenii (Characidae) in a reservoir of the Canela National Forest, Brazil. Journal of Freshwater Ecology, 29(2), pp.295–299. doi: 10.1080/02705060.2013.879539.

Cholik, F., Artati & Arifudin, R., 1991. Water Quality Management of Fish Pond, Direktorat Jenderal Perikanan. Jakarta.

Central Government, 2001. PP No. 82.: Peraturan Pemerintah Republik Indonesia Tentang Pengelolaan Kualitas Air dan Pengelolaan Pencemaran Air, Jakarta.

Central Government, 2021. Government Regulation of Republic of Indonesia No. 22, 2021: Government Implementation of Environmental Protection and Management., Indonesia.

Effendi, H., 2003. Water Quality Study for Water Resources and Environmental Management, Yogyakarta: Kanisius.

Emawati, Y., Aida, S.N.A. & Juwaini, H., 2017. Reproductive biology of leaffish, Pristolepis grootii Blkr. 1852 (Nandidae) in the Musi River. Iktiologi Indonesia, 9(1), pp.13–24.

Froese, R. & Pauly, D., 2019. Species of Pristolepis. FishBase.

Hedrick, P.W., 2005. Genetics of Populations Third., Jones and Bartlett.

Holmes, S., 2003. Bootstrapping Phylogenetic Trees: Theory and Methods. Statistical Science, 18(2), pp.241–255. doi: 10.1214/ss/1063994979.

Hubert, N. et al., 2008. Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE, 3(6). doi: 10.1371/journal.pone.0002490.

Kimura, M., 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol, 15, pp.111–120.

Kottelat, M. & Whitten, A.J., 1993. Freshwater Fishes of Indonesian and Sulawesi, Periplus Editions Limited.

Kumar, S. et al., 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35, pp.1547–1549.

Lavoué, S. et al., 2020. Genetic evidence for the recognition of two allopatric species of Asian bronze featherback Notopterus (Teleostei, Osteoglossomorpha, Notopteridae). Zoosystematics and Evolution, 96(2), pp.449–454. doi: 10.3897/zse.96.51350.suppl2.

Lemey, P., Selemi, M. & Vandamme, A.M., 2009. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Cambridge-UK: Cambridge University Press.

Masters, J.C. et al., 2007. Phylogenetic relationships among the lorisoidea as indicated by craniodental morphology and mitochondrial sequence data. American Journal of Primatology, 69(1), pp.6–15. doi: 10.1002/ajp.20322.

Muladno, 2010. Genetic EngineeringTechnology, Bogor: IPB Press.

Muliani, D.R. et al., 2020. Characteristics of Crassostrea Oyster Cytochrome Oxidase Subunit I (COI) Gene as Species Identity In Delta Cimanuk, West Java. Jurnal Moluska Indonesia, 4(1), pp.8–16.

Muslim, M. et al., 2019. Introduction to know the leaffish (Pristolepis grootii), a species native to Indonesia, a candidate commodity for aquaculture doi: 10.33087/aquaculture.v4i2.52. Jurnal Akuakultur Sungai dan Danau, 4(2).

Muslim, M. & Syaifudin, M., 2022. Biodiversity of Freshwater Fish in Kelekar Floodplain Ogan Ilir Regency in Indonesia.Journal of Tropical Biodiversity and Biotechnology, 7(1), jtbb.67494. doi: 10.22146/jtbb.67494.

Noikotr, K., 2019. Pristolepis fasciata Voucher FNP014 Cytochrome C Oxidase Subunit I (COI) Gene, Partial cds; Mitochondrial. Biology, Ramkhamhaeng University.Bangkok, Thailand., https://www.ncbi.nlm.nih.gov/nuccore/1607272014. Available at: https://www.ncbi.nlm.nih.gov/nuccore/1607272014 [Accessed January 3, 2022].

Pramono, et.al. 2019. Genetic characteristics of Senggaringan fish (Mystus singarngan) from Klawing River, Brantas River and Thailand as basis of conservation and domestication. AACL Bioflux, 12(4), pp.996-1004.

Pérez-Coyotl, I. et al., 2017. DNA damage and cytotoxicity induced on common carp by pollutants in water from an urban reservoir. Madín reservoir, a case study. Chemosphere, 185, pp.789–797. doi: 10.1016/j.chemosphere.2017.07.072.

Rubin, B.E.R., Ree, R.H. & Moreau, C.S., 2012. Inferring phylogenies from RAD sequence data. PloS one, 7(4), e33394. doi: 10.1371/journal.pone.0033394.

Stecher, G. et al., 2020. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Molecular Biology and Evolution, 37, pp.1237-1239.

Supartiwi, E.N., 2000. Characteristics of the phytoplankton and periphyton communities as indicators of the environmental quality of the Ciujung River, West Java, Bogor: IPB Press.

Syaifudin, M. et al., 2017. DNA authentication of asian redtail catfish Hemibagrus nemurus from Musi and Penukal River, South Sumatra Indonesia. Genetics of Aquatic Organisms, 1(December), pp.43–48. doi: 10.4194/2459-1831-v1.

Syaifudin, M. et al., 2019. DNA barcoding of snakeskin gourami Trichogaster pectoralis and blue gourami Trichogaster trichopterus based on cythocrome c oxidase subunit i (COI) gene. IOP Conference Series: Earth and Environmental Science, 348(1). doi: 10.1088/1755-1315/348/1/012031.

Syaifudin, M. et al., 2020. DNA barcodes and phylogenetic of striped snakehead and ocellated snakehead fish from South Sumatra, Indonesia. Biodiversitas, 21(3), pp.1227–1235. doi: 10.13057/biodiv/d210350.

Tindi, M. et al., 2017. DNA Barcode dan analisis filogenetik molekuler beberapa jenis bivalvia asal perairan Sulawesi Utara berdasarkan gen COI. Jurnal Pesisir Dan Laut Tropis, 5(2), p.32. doi: 10.35800/jplt.5.2.2017.15050.

Truong, O.T., Pham, P.T. & Dang, B.T., 2020. The 3rd International Conference on Sustainable Agriculture and Environment. In Species Diversity and Molecular Philogeny Of Perciformes in Mekong Delta, Vietnam. Ho Chi Minh: Nong Lam University.

Wang, T. et al., 2020. DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau. BMC Evolutionary Biology, 20(1). doi: 10.1186/s12862-020-01718-0.

Ward, R.D. et al., 2005. DNA barcoding Australia’s fish species. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 360(1462), pp.1847–57. doi: 10.1098/rstb.2005.1716.

Weber, M. & Beaufort., L.F. de, 1936. The Fishes of The Indo-Australian Archipelago VII: 479-80., E.J. Brill. Leiden.

Wijaya, F., 2001. Optimizing the use of production factors in the cultivation of catfish (Pangasius pangasius) with cage systems (in the waters of the Ogan River and Kelekar River, OKI Regency, South Sumatra)., Bogor.

Wong, E.H.K. & Hanner, R.H., 2008. DNA barcoding detects market substitution in North American seafood. Food Research International, 41(8), pp.828–837. doi: 10.1016/j.foodres.2008.07.005.



DOI: https://doi.org/10.22146/jtbb.74133

Article Metrics

Abstract views : 504 | views : 390

Refbacks

  • There are currently no refbacks.


Copyright (c) 2023 Journal of Tropical Biodiversity and Biotechnology

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Editoral address:

Faculty of Biology, UGM

Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia

ISSN: 2540-9581 (online)