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

Abstract

<jats:p>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).</jats:p>

Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene

“…This study supports the utility of the cytochrome b gene in phylogenetic relationships between Kryptopterus, Ompok, and Phalacronotus. This is in accordance with the results of molecular phylogenetic research that has been carried out on various species in the genus Puntius (Pallavi et al 2012), Pangasiidae and Schilbidae (Karinthanyakit and Jondeung 2012) and also catfish species in the family of Bagridae, Pangasiidae, and Ariidae (Megarani et al 2020).…”

“…The research on cytochrome b in Indonesia has been carried out on Chanos chanos (Adiputra et al 2011), Puntius cf. binotatus (Karlina et al 2016), Osphronemus goramy (Nugroho et al 2019), Bagridae, Pangasiidae and Ariidae (Megarani et al 2020). Research on the cytochrome b gene in silurid catfishes is very scarce in Indonesia; in fact, cytochrome b data for O. eugeneiatus and O. hypophthalmus have not been in GenBank until now (updated on December 9 th of 2019).…”

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

“…In this research, samples from Bengawan Solo River, Bojonegoro, East Java and from Elo River, Magelang, Central Java had high number of nucleotides differences as well as the amino acid variation. These results supported the confirmation that the samples were different species based on cytochrome-B and cytochrome oxidase subunit III gene (Widayanti et al 2019;Megarani et al 2020) whereas samples from the Progo River, Magelang, Central Java were less different and closer to the samples from other rivers from the different islands. These results strengthen the hypothesis that distinguishes the species based on morphological features is not fully accurate so that geneticbased identification is needed.…”

“…Previous studies reported that geographical aspects in Indonesian lands influenced the speciation of catfish and resulted in genetic diversity of catfishes based on cytochrome-B and cytochrome oxidase subunit II gene (Widayanti et al 2019;Megarani et al 2020). Based on the previous reports, phylogenetic analysis using the DNA sequences is needed to reveal accurate species identification and support the conservation program.…”

“…Previous studies reported that indigenous catfish of Indonesia classified into Hemibagrus nemurus, which belong to Bagridae family, but there are some species that allocated in the Pangasiidae family based on cytochrome oxidase subunit III and species from Papua that belong to Ariidae family based on cytochrome B gene (Syaifudin et al 2017;Widayanti et al 2019;Megarani et al 2020). Genetic analysis itself recently highlighted related to the possibility for applications in fishery genetics (Kochzius 2009).…”