Genetic diversity of indigenous catfish from Indonesia based on mitochondrial Cytochrome Oxidase Subunit II gene




Abstract. Budiariati V, Susmiati T, Waroh S, Putri RCA, Widayanti R. 2021. Genetic diversity of indigenous catfish from Indonesia based on mitochondrial Cytochrome Oxidase Subunit II gene. Biodiversitas 22: 593-600. Catfish is one of the most demanding fish in Indonesia and served in a variety of traditional culinary. Due to their identical morphology and close relation between species in the order of Siluriformes, it is quite tricky to distinguish the species. This can be a threat to develop catfish production in Indonesia since there is a wide variety of catfish species in this mega biodiversity country. The study aimed to analyze the genetic diversity of Indonesian indigenous catfish especially those known as Baung fish by local people based on COII gene. The study also aimed to determine the phylogenetic relationship between the samples and compare them with the GenBank data. A total of 24 samples used in this study from 8 different rivers from 3 different islands and two samples were collected from coastal areas. The study results showed that there is genetic diversity of the Indonesian indigenous catfish based on COII gene. The sequences among 24 samples showed that from 691 nucleotides of COII gene, there were very subtle nucleotides differences of samples that originated from Bojonegoro, Magelang, and samples collected from Baru Beach, Yogyakarta. Based on COII amino acid sequences, 6 polymorphic amino acid sites were on-site number 64, 115, 123, 129, 144, and 165. The samples encoded LLB1 and LPB1 from Baru Beach, Yogyakarta, showed highest different amino acids in the six sites. Samples from the river of Central Java, Sumatra, and Kalimantan belonged to Bagridae family and consist of two different species Hemibagrus sp. and Mystus sp while samples from East Java belonged to Pangasiidae family. The Samples from coastal belonged to Ariidae family.


Arce M, Reis RE, Geneva AJ, Pérez MHS. 2013. Molecular phylogeny of thorny catfishes (Siluriformes: Doradidae). Mol. Phylogenet. Evol. 67: 560–577.
Armbruster JW. 2004. Phylogenetic relationships of the suckermouth armoured catfishes (Loricariidae) with emphasis on the Hypostominae and the Ancistrinae. Zool. J. Linnean Soc. 141: 1–80.
Buj I., Šanda R, Mar?i? Z, ?aleta M, Mrakov?i?, M. 2014. Combining morphology and genetics in resolving taxonomy-a systematic revision of spined loaches (genus Cobitis; Cypriniformes, Actinopterygii) in the Adriatic watershed. PLoS One 9(6): e99833.
Denadai MR, Bessa E, Santos FB, Fernandez WS, Santos FMC, Feijo MM, Arcuri ACD, Turra A. 2012. Life history of three catfish species (Siluriformes: Ariidae) from Southeastern Brazil. Biota Neotrop 12(4): 74-83.
Dodson JJ, Colombani F, Ng PKL. 1995. Phylogeographic structure in mitochondrial DNA of a South-East Asian freshwater fish, Hemibagrus nemurus (Siluroidei; Bagridae) and Pleistocene sea-level changes on the Sunda shelf. Mol. Ecol 4(3): 331-346.
Dodson JJ. 1999. Morphological and genetic descrip¬tion of a new species of catfish, Hemibagrus chrysops, from Sarawak, East Malaysia, with an assessment of phy¬logenetic relationships (Teleostei: Bagridae). Raffles. Bull. Zool. 47(1): 45-58.
Ferraris CJ. 2007. Checklist of catfishes, recent and fossil (Osteichthyes: Siluriformes), and catalog of Siluriform pri¬mary types. Zootaxa 1418(1): 1-628.
Jin Y, Liu S, Yuan Z, Yang Y, Tan S, Liu Z. 2016. Genomics in Aquaculture Catfish Genomic Studies: Progress and Perspectives. Elsevier Inc.
Kappas I, Vittas, Pantzartzi CN, Drosopoulou E, Scouras ZG. 2016. A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes). PLoS ONE 11(12): 1–16.
Kawiji, Anam C, Parnanto N, Ariyoga UN. 2020. Catfish (Pangasius Sp.) as a Protein Source in Increasing Instant Baby Food (MpasI) Quality with Freeze Drying Method. AIP Conference Proceedings 2219(May): 3–8.
Kirk H and Freeland JR. 2011. Applications and Implications of Neutral versus Non-Neutral Markers in Molecular Ecology. International Journal of Molecular Sciences 12(6): 3966–88.
Kumar S, Stecher G. Li M, Knyaz C, Tamura, K. 2018. MEGA X: Molecular evolutionary genetics anal¬ysis across computing platforms. Mol. Biol. Evol. 35(6): 1547-1549.
Liu Z. 2008. Catfish. In: Thomas, K.D., Chittaranjan, K. (Eds.), Genome Mapping and Genomics in Fishes and Aquatic Animals Volume 2. Berlin Heidelberg. pp. 85–100.
Liu Z. 2011. Development of genomic resources in support of sequencing, assembly, and an¬notation of the catfish genome. Comp. Biochem. Physiol. Part D Genomics Proteomics 6: 11–17.
Megarani DV, Nugroho HA, Andarini ZP, Surbakti YDRBR, Widayanti R. 2020. Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene. Veterinary World 13(1): 96-103.
Mesomya W, Cuptapun Y, Jittanoonta P, Hengsawadi D, Boonsivut S, Huttayanon P, Sriwatana W. 2002. Nutritional evaluations of green catfish, Mystus nemurus. J. Nat. Sci. 36(1): 69-74.
Ng, HH and Kottelat M. 2013. Revision of the Asian catfish genus Hemibagrus Bleeker, 1862 (Teleostei: Siluriformes: Bagridae). Raffles. Bull. Zool. 61(1): 205-291.
Syaifudin M, Jubaedah D, Muslim M, Daryani A. 2018. DNA authentication of Asian redtail catfish Hemibagrus nemurus from Musi and Penukal river, South Sumatra Indonesia. Genet. Aquat. Organ 1(1): 43-48.
Widayanti R, Haryanto A, Artama WT, Pakpahan S. 2019. Genetic variation and phylogenetic analysis of Indonesian indigenous catfish based on mitochondrial cyto¬chrome oxidase subunit III gene. Veterinay World 12(6): 896-900.
Wilson DE, and Reeder DM. 2005. Mammal Species of the World: a Taxonomic and Geograph¬ic Reference, third ed. Johns Hopkins University Press, Baltimore, Maryland.