Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene

Research (Published online: 13-01-2020)

14. Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene

Dorothea Vera Megarani, Herjuno Ari Nugroho, Zahrah Prawita Andarini, Yura Dwi Risa B. R. Surbakti and Rini Widayanti

Veterinary World, 13(1): 96-103

Dorothea Vera Megarani: Department of Clinical Pathology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.

Herjuno Ari Nugroho: Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, West Java, Indonesia.

Zahrah Prawita Andarini: Veterinary Medicine Undergraduate Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.

Yura Dwi Risa B. R. Surbakti: Veterinary Medicine Undergraduate Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.

Rini Widayanti: Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.

doi: www.doi.org/10.14202/vetworld.2020.96-103

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Article history: Received: 09-09-2019, Accepted: 09-12-2019, Published online: 13-01-2020

Corresponding author: Rini Widayanti

E-mail: rini_widayanti@ugm.ac.id

Citation: 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.

Abstract

Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences.

Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software.

Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids).

Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).

Keywords: cytochrome B, Indonesian indigenous catfish, mitochondrial DNA, phylogenetic study, Siluriformes.