Assessing the species composition of tropical eels (Anguillidae) in Aceh Waters, Indonesia, with DNA barcoding gene cox1.

Muchlisin, Zainal A.; Batubara, Agung Setia; Fadli, Nur; Muhammadar, Abdullah A.; Utami, Afrita Ida; Farhana, Nurul; Nor, Siti Azizah Mohd

doi:10.12688/f1000research.10715.1

“…The study on DNA barcoding for freshwater fish has been widely practiced in various countries, including Nigeria 14 , India 15 , Philippines 16 , Canada 9 and Indonesia 5,[17][18][19] . The method has been successfully validated for the taxonomic status within Rasbora in Lake Laut Tawar 20 ; Anguillidae in Aceh waters 21 ; Ornamental fish from Peat lands 5 ; Channidae in Peninsular Malaysia, Sarawak, Sumatera, Borneo, Myanmar, Vietnam, India, Germany, Singapore and the United Kingdom 22 and Cichlidae in northeastern Nigeria 23 ; therefore, it can be used to equally successfully validate the taxonomic unit of the kelabau using its morphology supported by molecular data. This information is crucial for designing a remedial course of action about the conservation strategy for this species in the Siak, Kampar and Rokan rivers in Riau Province, Indonesia.…”

Section: Introductionmentioning

confidence: 99%

Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Asiah

¹

,

Junianto

²

,

Yustiati

³

et al. 2020

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Background: Kelabau (Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 (CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%–97% in GenBank and 96.6%–96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

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“…Saat ini penggunaan DNA mitokondria untuk karakterisasi genetik pada ikan telah banyak dilakukan antara lain pada ikan belut (Monopterus albus) (Arisuryanti, 2016;Arisuryanti et al, 2016); ikan arowana (Scleropages formosus) (Ngili et al, 2015) dan ikan sidat (Anguila sp.) (Muchlisin et al, 2017). Penelitian karakterisasi genetik ikan gabus menggunakan gen mitokondria 16S yang dilakukan oleh Lakra et al (2010) dan menggunakan gen mitokondria COI yang dilakukan oleh Aquino et al (2011), Benziger et al (2011), Serrao et al (2014), Sood et al (2015), Dhar & Ghosh (2015), dan Dahruddin et al (2016) membuka kesempatan lebih jauh untuk melakukan kajian gen mitokondria yaitu dengan mengamati komposisi nukleotidanya terutama bagi ikan gabus yang ditemukan di Danau Sentani, Jayapura, Papua yang belum pernah diteliti sebelumnya.…”

unclassified

The 16S and COI Mitochondrial DNA Nucleotide Composition of Stripped Snakehead (Channa striata Bloch,1793) from Lake Sentani, Jayapura, Papua

Kombong

¹

,

Arisuryanti

²

2019

JFS

4

1

0

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Stripped snakehead (Channa striata Bloch,1793) has potency to be developed in Indonesia due to high nutritional value including omega 3 which is useful for children growth. However, study on composition of mitochondrial DNA nucleotide as a part of study on genetic characterization of stripped snakehead fish in Indonesia is poorlyunderstood. Genetic characterization of stripped snakehead is important to obtain data information that can be applied for breeding and conservation program. Therefore, the objective of this study was to determine the 16S and COI mitochondrial DNA nucleotide of stripped snakehead collected from Lake Sentani, Jayapura, Papua. Method used in this research is PCR method using primer 16Sar and 16Sbr for 16S mitochondrial gene, and FishF2 and FishR2 for COI mitochondrial gene. The results showed that composition of 16S mtDNA nucleotide from 616 bp was T=21.92%, C=25.49%, A=30.19%, dan G=22.40%, whereas composition of A+T=52.11% and G+C=47.89%. In addition, composition of COI mtDNA nucleotide from 705 bp was T=29.93%, C=28.65%, A=24.26%, and G=17.16% while composition of A+T=54.48% and G+C=45.52%. Data of 16S and COI mitochondrial DNA nucleotide composition of the stripped snakehead collected from Lake Sentani gained in this study are to be expected to complete genetic information of the fish species which is useful to improve breeding program of this fish species in the future.

show abstract

“…The study on DNA barcoding for freshwater fish has been widely practiced in various countries, including Nigeria 14 , Malaysia 15 , Philippines 16 , Canada 9 and Indonesia 5,[17][18][19] . The method has been successfully validated for the taxonomic status within Rasbora in Lake Laut Tawar 20 ; Anguillidae in Aceh waters 21 ; Ornamental fish from Peat lands 5 ; Channidae in Peninsular Malaysia, Sarawak, Sumatera, Borneo, Myanmar, Vietnam, India, Germany, Singapore and the United Kingdom 22 and Cichlidae in northeastern Nigeria 23 ; therefore, it can be used to equally successfully validate the taxonomic unit of the kelabau using its morphology supported by molecular data. This information is crucial for designing a remedial course of action about the conservation strategy for this species in the Siak, Kampar and Rokan rivers in Riau Province, Indonesia.…”

Section: Introductionmentioning

confidence: 99%

Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Asiah¹,

Junianto²,

Yustiati³

et al. 2020

F1000Res

Self Cite

0

View full text Add to dashboard Cite

Background: Kelabau (Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 (CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%–97% in GenBank and 96.6%–96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

show abstract

Assessing the species composition of tropical eels (Anguillidae) in Aceh Waters, Indonesia, with DNA barcoding gene cox1.

Cited by 27 publications

References 14 publications

Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

The 16S and COI Mitochondrial DNA Nucleotide Composition of Stripped Snakehead (Channa striata Bloch,1793) from Lake Sentani, Jayapura, Papua

Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

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