Identification, genetic diversity, and comparative evolution of the striped snakehead Channa striata (Bloch, 1793) in Wallacea, Indonesia

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IRMAWATI
MEIMULYA
ASMI CITRA MALINA A. R. TASSAKKA
NADIARTI
NITA RUKMINASARI
INCE AYU KHAIRANA KADRIAH
HASAN NASRULLAH
ALIMUDDIN

Abstract

Abstract. Irmawati, Meimulya, Tassakka ACMAR, Nadiarti, Rukminasari N, Kadriah IAK, Nasrullah H, Alimuddin. 2022. Identification, genetic diversity, and comparative evolution of the striped snakehead Channa striata (Bloch, 1793) in Wallacea, Indonesia. Biodiversitas 23: 3327-3337. Striped snakehead, Channa striata populations have declined in some areas of Wallacea. This study aimed to identify the species, analyze the genetic diversity, and trace the evolutionary relationships of snakeheads in the Wallacea region with snakeheads in other geographic areas. This study was identifying all specimens in this study as C. striata. The Wallacean C. striata sequences comprised three haplotypes with five polymorphic sites (single nucleotide polymorphisms, SNPs). No mutations were detected in the COI nucleotides of C. striata in the Tempe Lake complex, Patampanua River, and Bojo River; therefore, they belonged to the same haplotype. The C. striata from the Tangkoli tertiary drainage had unique haplotypes that differed from other C. striata haplotypes. The intraspecific genetic distance within C. striata was low while the interspecific genetic distance within the genus Channa was quite large, indicating that mutation rates are quite high in the genus Channa. Haplotype evolution showed that C. striata in Wallacea shared a common ancestral pathway with C. striata in Kalimantan, Java, and Bali and had a different ancestral pathway with C. striata in Lampung (Sumatra). The nucleotide composition of the C. striata COI gene followed the general pattern of the Teleostei and the Pisces superclass (T>C>A>G) with the G+C base percentage lower than the A+T percentage. The data from this study will be useful as a basis for designing germplasm conservation strategies and designing strategies to maintain C. striata populations and develop strains to meet future needs.

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References
Abol-Munafi AB, Ambak MA, Ismail P MinhTam B. 2007. Molecular Data from the Cytochrome b for the Phylogeny of Channidae (Channa sp.) in Malaysia. Biotechnology, 6(1):22-27.
Alam MS, Projna F, Zafrin MS, Das R, Khan MGQ. 2022. Assessment of genetic diversity, detection of strain-specific single nucleotide polymorphisms and identification of the Bangladesh and Vietnam strain of Channa striata by PCR-RFLP analysis of the mitochondrial COI gene fragment. Aquaculture and Fisheries 7:287–295. DOI: 10.1016/j.aaf.2020.12.006.
Ali D, Nagpure NS, Kumar S, Kumar R, Kushwaha B, Lakra WS. 2009. Assessment of genotoxic and mutagenic effects of chlorpyrifos in freshwater fish Channa punctatus (Bloch) using micronucleus assay and alkaline single-cell gel electrophoresis. Food and Chemical Toxicology 47(3):650-656. DOI: 10.1016/j.fct.2008.12.021.
Arthington AH, Dulvy NK, Gladstone W, Winfield IJ. 2016. Fish conservation in freshwater and marine realms: status, threats and management. Aquatic Conservation: Marine and Freshwater Ecosystems 26(5):838-857. DOI: 10.1002/aqc.2712.
Baisvar VS, Singh M, Kumar R. 2019. Population structuring of Channa striata from Indian waters using control region of mtDNA Population structuring of Channa striata from Indian waters using control region of mtDNA. Mitochondrial DNA Part A 0(0): 1–10. DOI:10.1080/24701394.2018.1532416.
Bandelt HJ, Forster P, Ro A. 1999. Median-Joining Networks for Inferring Intraspecific Phylogenies. Molecular Microbiology 16:37–48.
Barbhuiya PA, Uddin A, Chakraborty S. 2020. Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia. Journal of Cellular Physiology 236(4):2850-2868. DOI: 10.1002/jcp.30050.
Boonkusol D, Tongbai W. 2016. Research Article Genetic Variation of Striped Snakehead Fish (Channa striata) in River Basin of Central Thailand Inferred from mtDNA COI Gene Sequences Analysis. Journal of Biological Sciences 16(1):37–43. DOI:10.3923/jbs.2016.37.43.
Brown WM, Prager EM, Wilson AC. 1982 Mitochondrial DNA sequences of primates, tempo and mode of evolution. Journal of Molecular Evolution 18:225–239.
Chakrabarty D, Das SK. 2006. Fish community structure and ecological degradation in tropical rivers of India. Web Ecology. 6(1):27-36.
Chakraborty S, Uddin A, Mazumder TH, Choudhury MN, Malakar AK, Paul P, Halder B, Deka H, Mazumder GA, Barbhuiya RA, Barbhuiya MA, Devia WJ. 2018. Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents. Mitochondrion 42:64-76.
Chaudhry S, Goonatilake DA, Fernado M, Kotagama O. 2019. Channa striata, Snakehead Murrel. The IUCN red list of threatened species.
Cong NV, Phuong NT, Bayley M. 2009. Effects of repeated exposure of diazinon on cholinesterase activity and growth in snakehead fish (Channa striata). Ecotoxycology and environmental safety, 72:699-703. DOI: 10.1016/j.ecoenv.2008.10.007.
Conte-Grand C, Britz R, Dahanukar N, Raghavan R, Pethiyagoda R, Tan HH, Hadiaty RK, Yaakob NS, Rüber L. 2017. Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions. PLOS ONE 12:e0184017. DOI: 10.1371/journal.pone.0184017.
Curtis SE, Clegg MT. 1984. Molecular evolution of chloroplast DNA sequences. Molecular Biology and Evolution 1:291–301.
Dahruddin H, Hutama A, Busson F, Sauri S, Hanner R, Keith P, Hadiaty R, Hubert N. 2017. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Molecular Ecology Resources 17:288–299. DOI: 10.1111/1755-0998.12528.
Dayal R., Srivastava PP, Bhatnagar A, Raizada S, Chowdhary S, Yadav AK, Lakra WS. 2013. Captive spawning of the striped murrel, Channa striatus (Bloch) using sGnRH, in Gangetic plains of India; Proceedings National Academy Sciences India B: Biology Science. January–March 2013. [India].
Diana JS, Chang WYB, Ottey DR, Chuapoehuk W. 1985. Production systems for commonly cultured freshwater fishes of Southeast Asia. International Programme Report, The University of Michigan 7:75-79.
Duong TY, Uy S, Chheng P, So N, Tran THT, Thi NT, Pomeroy R, Egna H. 2019. Genetic diversity and structure of striped snakehead (Channa striata) in the Lower Mekong Basin: Implications for aquaculture and fisheries management. Fisheries Research, 166-173. DOI: 10.1016/j.fishres.2019.05.014.
Funk WC, McKay JK, Hohenlohe PA, Allendorf FW. 2012. Harnessing genomics for delineating conservation units. Trends in Ecology & Evolution. 27(9):489-496. DOI: 10.1016/j.tree.2012.05.012.
Gojobori T, Li W, Graur D. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. Journal of Molecular Evolution 18:360–369.
Gustiano R, Oktaviani T, Soelistyowati DT, Kusmini II. 2013. Analisis ragam genotip RAPD and fenotip truss morfometrik pada tiga populasi ikan gabus Channa striata (Bloch , 1793). Berita biologi 12(3):325–333.
Haniffa MA, Marimuthu K, Nagarajan M. 2004. Breeding behaviour and parental care of the induced bred spotted murrel Channa punctatus under captivity. Current Science 8(6):1375–1376.
Harianti. 2013. Fecundity and egg diameter of stripped snakehead (Channa striata Bloch, 1793) in Tempe Lake, Wajo. Journal of Fisheries Science 8(2):18-24.
Hebert PDN, Gregory TN. 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54(5): 852–859. DOI: 10.1080/10635150500354886.
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PloS Biology 2(10):1657-1663. DOI: 10.1371/journal.pbio.0020312
Hien TTT, Be TT, Lee CM, Bengtson DA. 2015. Development of formulated diets for snakehead (Channa striata and Channa microleptes): Can phytase and taurine supplementation increase use of soybean meal to replace fish meal. Aquaculture, 448:334-340. DOI: 10.1016/j.aquaculture.2015.06.020
Hossain MK, Latifa GA, Rahman MM. 2008. Observations on induced breeding of snakehead murrel, Channa striatus (Bloch, 1793). International Journal of Sustainable Crop Production 3(5):65–68.
Hubert N, Meyer CP, Bruggemann HJ, Guérin F, Komeno RJL, Espiau B, Causse R, Williams JT, Planes S. 2012. Cryptic diversity in Indo Pacific coral reef fishes revealed by DNA barcoding provides new support to the centre of overlap hypothesis. PloS One 7:e28987. DOI: 10.1371/journal.pone.0028987
Irmawati. 1994. Struktur komunitas ikan and aspek biologi ikan-ikan dominan di Danau Sidenreng, Sulawesi Selatan. [Bachelor Thesis] Bogor (ID): IPB University.
Irmawati, Tresnati J, Nadiarti, Yunus B, Utami MS. 2017a. The characterization of snakehead (Channa sp.) from Bantimurung River, Maros Regency, South Sulawesi. Prosiding of Simposium Nasional IV Kelautan dan Perikanan 1, Makassar, 19 Mei 2017.
Irmawati, Tresnati J, Nadiarti, Fachruddin L, Arma NR, Haerul A. 2017b. Identification of wild stock and the first generation (F1) of domesticated snakehead fish, Channa spp. (Scopoli 1777) using partial Cytochrome C Oxidase Subunit I (COI) gene. Jurnal Iktiologi Indonesia 17(2):165–173.
Irmawati, Umar MT, Ambo A, Husain A. 2020. Distribution and characteristics of Asian seabass (Lates calcarifer Bloch, 1790 ) in South Sulawesi. IOP conference series: Earth and Environmental Science. Proceeding of The 3rd International Symposium of Marine and Fisheries. Makassar, 6 June 2020. DOI: 10.1088/1755-1315/564/1/012011.
Irmawati, Tresnati J, Fachruddin L. 2019. Sex Differentiation and Gonadal Development of striped snakehead (Channa striata Bloch, 1793). IOP Conference Series: Earth and Environmental Science. Proceeding of The 2nd International Symposium of Marine and Fisheries. Makassar. DOI: 10.1088/1755-1315/253/1/012007.
Jamaluddin JAF, Pau TM, Siti-Azizah MN. 2011. Genetic structure of the snakehead murrel, Channa striata (Channidae) based on the cytochrome c oxidase subunit I gene: Influence of historical and geomorphological factors. Genetic and Molecular Biology, 34(1):152-160.
Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-120.
Kitanishi S, Onikura N, Mukai T. 2018. A simple SNP genotyping method reveals extreme invasions of non-native haplotypes in pale chub Opsariichthys platypus, a common cyprinid fish in Japan. PloS one, 13(1):e0191731
Kombong CBS, Arisuryanti T. 2018. The 16S and COI Mitochondrial DNA Nucleotide Composition of Stripped Snakehead (Channa striata Bloch,1793) from Lake Sentani, Jayapura, Papua. Jurnal Perikanan Universitas Gadjah Mada, 20(2):57-62. DOI: 10.22146/jfs.355
Kumar K, Eknath AE, Sahu AK, Mohanty UL, Kumar R, Sahoo M, Jahan N. 2011. Snakeheads: challenging fish for diversification of fish farming. Fish. Chimes 31 (1):110–113.
Kumar R, Gokulakrishnan M, Debbarma J, Damle DK. 2022. Advances in captive breeding and seed rearing of striped murrel Channa striata, a high value food fish of Asia. Animal Reproduction Science, 106957 (in press). DOI: 10.1016/j.anireprosci.2022.106957
Kumar S, Stecher G, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35 (6): 1547-1549.
Kumari S, Tiwari VK, Rani AMB, Rajesh K, Satya P. 2018. Effect of feeding rate on growth, survival and cannibalism in striped snakehead, Channa striata (Bloch, 1793) fingerlings. Journal of Experimental Zoology 21(1):205–210.
Lakra WS, Gowami M, Gopalakrishnan A, Singh DP. 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
Lamolle G, Iriarte A, Musto H. 2022. Codon usage in the flatworm Schistosoma mansoni is shaped by the mutational bias towards A+T and translational selection, which increases GC-ending codons in highly expressed genes. Molecular and Biochemical Parasitology, 247:111445. DOI: 10.1016/j.molbiopara.2021.111445.
Li X, Musikasinthorn P, Kumazawa Y. 2006. Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences. Ichthyological Research 53(2):148-159. DOI: 10.1007/s10228-005-0321-3
Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452. DOI: 10.1093/bioinformatics/btp187.
Ling SW. 1977. Snakehead, Ophiocephalus spp. Culture. In: Aquaculture in Southeast Asia: A Historical Overview, Ling SW (ed.). University of Washington Press, Seattle, WA.USA. pp 60-66.
Liu K, Ouyang Y, Lin R, Ge C, Zhou M. 2022. Strong negative correlation between codon usage bias and protein structural disorder impedes protein expression after codon optimization. Journal of Biotechnology, 343:15-24. DOI: 10.1016/j.jbiotec.2021.11.001.
Lynch M, Jarrell PE. 1993. A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Journal Genetics 135(4):1197–1208.
Marko PB, Lee S, Rice AM, Gramling JM, Fitzhenry TM, McAlister JS. 2004. Mislabeling of a depleted reef fish. Nature 430:309–310. DOI: 10.1038/nature02689.
Muhajirah E, Kamal MM, Butet NA, Wibowo A. 2021. Keragaman genetic populasi giant Snakehead (Channa micropeltes) menggunakan penanda Random Amplified Polymorphic DNA di perairan Taman Nasional Sebangau, Kalimantan Tengah. Journal of Natural Resources and Environmental Management 11(1):141–151.
Muntaziana MPA, Amin SMN, Rahman MA, Rahim AA, Marimutu K. 2013. Present culture status of the endangered snakehead, Channa striatus (Bloch, 1793). Asian Journal os Animal and Veterinary Advances 8(2):369-375. DOI: 10.3923/ajava.2013.369.375.
Nariyampet SA, Hajamohideen AJ. 2019. A study on codon usage bias in cytochrome c oxidase I (COI) gene of solitary ascidian Herdmania momus Savigny, 1816. Gene Reports 17(100523):1-11. DOI: 10.1016/j.genrep.2019.100523.
Ndobe S, Serdiati N, Moore A. 2013. Upaya domestikasi melalui pembesaran ikan gabus (Channa striata) di dalam wadah terkontrol. Proceedings of Konperensi Akuakultur Indonesia 2013: 165-175
Pandey AK, Nagpure NS, Trivedi SP. 2018. Genotoxicity assessment of pesticide profenofos in freshwater fish Channa punctatus (Bloch) using comet assay and random amplified polymorphic DNA (RAPD). Chemosphere 211:316-323. DOI: 10.1016/j.chemosphere.2018.07.182.
Paripatananont T. 2002. Snakehead and Pangasius catfish. In: Webster, C.D., Lim, C.E. (Eds.), Nutrient requirements and feeding of finfish for aquaculture. CAB International, pp. 396–401.
Pavlova ., Beheregaray LB, Coleman R, Gilligan D, Harrisson KA, Ingram BA, Kearns J, Lamb AM, Lintermans M, Lyon J, Nguyen TTT, Sasaki M, Tonkin Z, Yen JDL, Sunnucks P. 2017. Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow. Evolutionary Applications 10(6):531–550. DOI: 10.1111/eva.12484.
Phan LTT, Masagounder K, Mas-Munoz JW, Schrama. 2020. Differences in energy utilization efficiency of digested protein, fat and carbohydrates in snakehead (Channa striata). Journal Aquaculture 532: 736066. DOI: 10.1016/j.aquaculture.2020.736066
Prehadi SA, Kurniasih EM, Rahmad, Arafat D, Subhan B, Madduppa HH. 2015. DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in Comparison with Southern Java fishing port. Biodiversitas 16(1):55–61. DOI: 10.13057/biodiv/d160107.
Rahim MHA, Ismail P, Alias R, Muhammad N, Jais AMM. 2012. PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia. Gene 494(1):1-10.
Ren A, Ishida T, Akiyama Y. 2013. Molecular Phylogenetics and Evolution Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method. Molecular Phylogenetics and Evolution, 67(2):429–435. DOI: 10.1016/j.ympev.2013.02.011.
Robert R, Amit NH, Sukarno NM, Majapun RJ, Kumar SV. 2018. Population genetic structure of Asian snakehead fish (Channa striata) in North Borneo: Implications for conservation of local freshwater biodiversity. Ecological Research 34(1):55-67.
Ryder OA. 1986. Species conservation and systematics: The dilemma of the subspecies. Trends in Ecology & Evolution 1:9–10.
Sahu SK, Thangaraj M, Kathiresan K. 2012. DNA extraction protocol for plants with levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. International Scholarly Research Network. 2012: 1-6. DOI: 10.5402/2012/205049.
Serrao NR, Steinke D, Hanner RH. 2014. Calibrating Snakehead Diversity with DNA Barcodes: Expanding Taxonomic Coverage to Enable Identification of Potential and Established Invasive Species. PLoS ONE 9:e99546. DOI: 10.1371/journal.pone.0099546.
Steinke D, Vences M, Salzburger W, Meyer A. 2005. TaxI: a software tool for DNA barcoding using distance methods. Philosophical Transactions of the Royal Society B-Biological Sciences 360:1975–1980. DOI: 10.1098/rstb.2005.1729
Syaifudin M, Wijayanti M, Dwinanti SH, Muslim M, Mahendra M, Marliana S. 2020. DNA barcodes and phylogenetic of striped snakehead and ocellated snakehead fish from South Sumatra, Indonesia. Biodiversitas Journal of Biological Diversity 21(3):1227-1235. DOI: 10.13057/biodiv/d210350.
Thompson JD, Toby JG, Frederic P, François J, Desmond GH. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25(24): 4876–4882.
Uddin A, Mazumder TH, Chakraborty S. 2018. Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: relevance to mitochondrial diseases. Journal of Cellular Physiology 234(5):6397-6413. DOI: 10.1002/jcp.27375
Verspoor E, Consuegra S, Fridjonsson O, Hjorleifsdottir S, Knox D, Olafsson K, Garcia de Leaniz C. 2012. Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar L.): an assessment of potential utility for determination of natal origin. ICES Journal of Marine Science 69(9):1625-1636.
Wakeley J. 1994. Substitution rate variation among sites and the estimation of transition bias. Molecular Biology Evolution 11:436–442.
Wang H, Susko E, Roger AJ. 2016. Split-specific Bootstrap Measures for Quantifying Phylogenetic Stability and the Influence of Taxon Selection. Molecular Phylogenetics and Evolution. DOI: 10.1016/j.ympev.2016.08.017.
Ward RD. 2009. DNA barcode divergence among species and genera of birds and fishes. Molecular ecology resources 9:1077-1085.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society. B: Biological Sciences 360(1462):1847–1857.
Yang Z, Yoder AD. 1999. Estimation of the Transition/Transversion Rate Bias and Species Sampling. Journal Molecular Evolution 48:274–283.
Zhao S, Zhang Q, Chen Z, Zhao Y, Zhong J. 2007. The factors shaping synonymous codon usage in the genome of Burkholderia mallei. Journal of Genetics and Genomics 34(4):362–372.

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