Genetic variation and phylogenetic analysis of Indonesian indigenous catfish based on mitochondrial cytochrome oxidase subunit III gene

Vet World Vol.12 June-2019 Article-26

Research Article

Veterinary World, 12(6): 896-900

https://doi.org/10.14202/vetworld.2019.896-900

Rini Widayanti¹, Aris Haryanto¹, Wayan Tunas Artama¹, and Suhendra Pakpahan²

1. Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia.
2. Biology Study Program, Faculty of Biotechnology, Duta Wacana Christian University, Yogyakarta, Indonesia.

Background and Aim: This study aimed to analyze the genetic variation and phylogenetic reconstruction of Indonesian indigenous catfish using mitochondrial cytochrome oxidase subunit III sequences.

Materials and Methods: A total of 19 samples of catfish were collected from seven rivers (Elo [EM], Progo [PM], Kampar [KR], Musi [MP], Mahakam [MS], Kapuas [KS], and Bengawan Solo [BSBJ]) in five different geographical locations in Indonesia. The genome was isolated from the tissue. Mitochondrial DNA cytochrome oxidase subunit III was amplified using polymerase chain reaction (PCR) with CO3F and CO3R primers. The PCR products were sequenced and continued to analyze genetic variation and phylogenetic relationship using MEGA version 7.0 software.

Results: Cytochrome c oxidase (COX)-III gene sequencing obtained 784 nucleotides encoding 261 amino acids. Sequenced COX-III gene fragments were aligned along with other catfish from Genbank using ClustalW program and genetic diversity among species was analyzed using the MEGA Version 7.0 software. Among all samples, there were substitution mutations at 78 nucleotide sites, and there were 14 variations in amino acids. Catfish from PM, KR, MP, and KS had the same amino acids as Hemibagrus nemurus (KJ573466.1), while EM catfish had eight different amino acids and catfish BSBJhad 12 different amino acids.

Conclusion: Indonesian catfish divided into four clades. BBSJ Catfish were grouped with Pangasianodon gigas, EM catfish were grouped with Mystus rhegma, and KS catfish were grouped with Hemibagrus spilopterus, while catfish MS, KR, PM, and MP were grouped with H. nemurus. Keywords: cytochrome c oxidase-III, Hemibagrus, Indonesian indigenous catfish, mitochondrial DNA, phylogenetic.

Keywords: cytochrome c oxidase-III, Hemibagrus, Indonesian indigenous catfish, mitochondrial DNA, phylogenetic.

How to cite this article: Widayanti R, Haryanto A, Artama WT, Pakpahan S (2019) Genetic variation and phylogenetic analysis of Indonesian indigenous catfish based on mitochondrial cytochrome oxidase subunit III gene, Veterinary World, 12(6): 896-900.

Received: 22-01-2019 Accepted: 09-05-2019 Published online: 27-06-2019

Corresponding author: Rini Widayanti E-mail: rini_widayanti@ugm.ac.id

DOI: 10.14202/vetworld.2019.896-900

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.