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

Widayanti, Rini; Haryanto, Aris; Artama, Wayan Tunas

doi:10.14202/vetworld.2019.896-900

Cited by 7 publications

(11 citation statements)

References 14 publications

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“…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.…”

Section: Variation Of Nucleotides and Amino Acids Sequencessupporting

confidence: 78%

“…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.…”

Section: Variation Of Nucleotides and Amino Acids Sequencesmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Variation Of Nucleotides and Amino Acids Sequencessupporting

confidence: 78%

Section: Variation Of Nucleotides and Amino Acids Sequencesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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“…Baung fish (Hemibagrus nemurus) is an essential commodity in Indonesia because it is widely consumed and contains essential nutrients. For example, baung fish are a valuable source of protein, lipids (with large amounts of omega-3, omega-6, monounsaturated fatty acids, docosahexaenoic acid, and eicosapentaenoic acid), minerals, albumin, and antioxidants [2][3][4].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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“…A previous study classified this particular catfish into Hemibagrus nemurus, which is in the Bagridae family [3]. Nonetheless, another study of Baung catfish originally from East Java Indonesia allocated this catfish into the Pangasiidae family based on the cytochrome C oxidase subunit 3 (COX-III) gene [4]. Therefore, further studies of the genetic markers of these indigenous catfishes, known as Baung catfish to local people in Indonesia, are needed to identify the catfish species and preserve their genetic resources.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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).

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

Cited by 7 publications

References 14 publications

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

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

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

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

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