Genetic variation and phylogenetic analysis of Indonesian indigenous catfish (baung fish) based on mitochondrial 12S rRNA gene

Vet World Vol.14 March-2021 Article-27

Research Article

Veterinary World, 14(3): 751-757

https://doi.org/10.14202/vetworld.2021.751-757

Rini Widayanti¹, Ken Ayik Kusumaastuti¹, Joana Martha Novi¹, Fadila Khairuna Adani¹, Catrine Relia Patrecia Gultom¹, Ayuning Devina Prastiti¹, Herjuno Ari Nugroho², and Suhendra Pakpahan²

1. Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.
2. Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Jakarta-Bogor KM 46, Cibinong, West Java, Indonesia.

Background and Aim: Baung fish is an essential commodity in Indonesia; however, few studies have explored the genetic diversity of Indonesian catfish. Thus, this study aimed to analyze the genetic variation and phylogenetic relationships among Indonesian catfish based on the mitochondrial 12S ribosomal RNA (rRNA) gene.

Materials and Methods: In total, 28 catfish were collected from nine rivers in seven provinces and from the Indian Ocean. Catfish genomes were obtained from epaxial and hepaxial muscle samples. The mitochondrial 12S rRNA gene was amplified by polymerase chain reaction using a pair of primers (Baung12SF and Baung12SR). The 12S rRNA sequences were analyzed using MEGA X to determine genetic variation and phylogenetic relationships.

Results: In total, 178 variation sites in the 12S rRNA gene were substituted among Indonesian catfish. The genetic distance between all Indonesian catfish samples was 0.1-16.0%. The closest genetic distance was between MP and PM catfish, whereas the farthest genetic distances were between BF and EM and PD and EM. For the entire population, based on mean diversity calculations, the number of base substitutions per site was 0.08.

Conclusion: Indonesian catfish were divided into four clades based on the 12S rRNA gene. The catfish MP, KR, PM, MS, BB, and KS were grouped with Hemibagrus nemurus, the catfish EM was grouped with Mystus vittatus, the catfish BSBJ was grouped with Pangasius pangasius, and the catfish PD and BF were grouped with Netuma thalassina. Keywords: 12S ribosomal RNA gene, baung fish, Hemibagrus nemurus, Indonesian catfish, phylogenetic.

Keywords: 12S ribosomal RNA gene, baung fish, Hemibagrus nemurus, Indonesian catfish, phylogenetic.

How to cite this article: Widayanti R, Kusumaastuti KA, Novi JM, Adani FK, Gultom CRP, Prastiti AD, Nugroho HA, Pakpahan S (2021) Genetic variation and phylogenetic analysis of Indonesian indigenous catfish (baung fish) based on mitochondrial 12S rRNA gene, Veterinary World, 14(3): 751-757.

Received: 20-11-2020 Accepted: 05-02-2021 Published online: 24-03-2021

Corresponding author: Suhendra Pakpahan E-mail: suhendrapakpahan@gmail.com

DOI: 10.14202/vetworld.2021.751-757

Copyright: Widayanti, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.