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DNA Barcoding and eDNA Metabarcoding for Identification Species: A Case Study (West Sumatra): DNA barcoding and eDNA metabarcoding

Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences · Vol. 15 No. 1 (2025) · hlm. 161–176

DOI
10.11594/jtls.15.01.16
ISSN
2527-4376, 2087-5517
Terbit
2025-06-26
Penerbit
Journal of Tropical Life Science
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-nc/4.0

Abstrak

The biodiversity of freshwater fish is important to study because there is data and information that remain undiscovered. The waters of Sumatra, especially West Sumatra, are areas with high freshwater fish diversity but have limited information. Providing information and genetic data has become one of the important things to conduct. DNA barcoding and eDNA metabarcoding have become molecular methods for identifying species and providing information about the presence of species in a region. A study using DNA barcoding and eDNA metabarcoding was conducted on freshwater fish in several locations in West Sumatra. Isolation and amplification of DNA were performed directly on individual samples and sequenced using conventional methods (Sanger sequencing) to generate DNA barcodes. Water samples were collected (2 liters) at each location using a sterile bottle. The water samples were filtrated, isolated, and amplified using universal primer and sequenced with next-generation sequencing techniques. The study successfully collected 25 species belonging to 14 genera, 2 families, and 1 order. A total of 134 sequences from West Sumatra with a length of 648-670 bp were analyzed. All DNA barcodes were submitted to the BOLD System and GenBank, NCBI. The mean Kimura two-parameter model (K2P) genetic distances within species, genera, families, and orders were 0.7%, 8.3%, 15.8%, and 21.3%, respectively. The eDNA metabarcoding technique has successfully detected three native fish species in the waters of West Sumatra (Barbonymus schwanefeldii, Mystacoleucus padangensis, and Rasbora jacobsoni). The availability of fish DNA barcodes in reference databases is crucial for the success of identification using eDNA metabarcoding. Combining identification using conventional methods and eDNA metabarcoding can provide more reliable results and become a reference for future freshwater monitoring.

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  • Universitas Jambi
  • Indonesia University of Education
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Rekan penulisOrganisasiArtikel bersama
Iim Siti MasyitohAfiliasi tidak diketahui1
Karim SuryadiAfiliasi tidak diketahui1
Fitriah ArtinaAfiliasi tidak diketahui1
Muhammad AminUniversitas Jambi1
Dasim BudimansyahIndonesia University of Education1
Sapriya SapriyaAfiliasi tidak diketahui1
Dikdik Baehaqi ArifAfiliasi tidak diketahui1

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Sumber metadata: OAI-PMH (metadata jurnal) http://jtrolis.ub.ac.id/index.php/jtrolis/oai, pertama di-harvest 9 Nov 2026, terakhir terlihat 9 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en">DNA Barcoding and eDNA Metabarcoding for Identification Species: A Case Study (West Sumatra): DNA barcoding and eDNA metabarcoding</dc:title>
	<dc:creator xml:lang="en">Roesma, Dewi Imelda</dc:creator>
	<dc:creator xml:lang="en">Tjong, Djong Hon </dc:creator>
	<dc:creator xml:lang="en">Syaifullah, Syaifullah</dc:creator>
	<dc:creator xml:lang="en">Nofrita, Nofrita</dc:creator>
	<dc:creator xml:lang="en">Janra, Muhammad Nazri</dc:creator>
	<dc:creator xml:lang="en">Aidil, Dyta Rabbani </dc:creator>
	<dc:creator xml:lang="en">Prawira, Furqan Dwiki Lintang </dc:creator>
	<dc:creator xml:lang="en">Salis, Viola Mutiara </dc:creator>
	<dc:subject xml:lang="en">BOLD System</dc:subject>
	<dc:subject xml:lang="en">DNA Barcoding</dc:subject>
	<dc:subject xml:lang="en">eDNA metabarcoding</dc:subject>
	<dc:subject xml:lang="en">Next Generation Sequencing</dc:subject>
	<dc:subject xml:lang="en">West Sumatra</dc:subject>
	<dc:description xml:lang="en">The biodiversity of freshwater fish is important to study because there is data and information that remain undiscovered. The waters of Sumatra, especially West Sumatra, are areas with high freshwater fish diversity but have limited information. Providing information and genetic data has become one of the important things to conduct. DNA barcoding and eDNA metabarcoding have become molecular methods for identifying species and providing information about the presence of species in a region. A study using DNA barcoding and eDNA metabarcoding was conducted on freshwater fish in several locations in West Sumatra. Isolation and amplification of DNA were performed directly on individual samples and sequenced using conventional methods (Sanger sequencing) to generate DNA barcodes. Water samples were collected (2 liters) at each location using a sterile bottle. The water samples were filtrated, isolated, and amplified using universal primer and sequenced with next-generation sequencing techniques. The study successfully collected 25 species belonging to 14 genera, 2 families, and 1 order. A total of 134 sequences from West Sumatra with a length of 648-670 bp were analyzed. All DNA barcodes were submitted to the BOLD System and GenBank, NCBI. The mean Kimura two-parameter model (K2P) genetic distances within species, genera, families, and orders were 0.7%, 8.3%, 15.8%, and 21.3%, respectively. The eDNA metabarcoding technique has successfully detected three native fish species in the waters of West Sumatra (Barbonymus schwanefeldii, Mystacoleucus padangensis, and Rasbora jacobsoni). The availability of fish DNA barcodes in reference databases is crucial for the success of identification using eDNA metabarcoding. Combining identification using conventional methods and eDNA metabarcoding can provide more reliable results and become a reference for future freshwater monitoring.</dc:description>
	<dc:publisher xml:lang="en">Journal of Tropical Life Science</dc:publisher>
	<dc:date>2025-06-26</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://jtrolis.ub.ac.id/index.php/jtrolis/article/view/3604</dc:identifier>
	<dc:identifier>10.11594/jtls.15.01.16</dc:identifier>
	<dc:source xml:lang="en">Journal of Tropical Life Science; Vol. 15 No. 1 (2025); 161 – 176</dc:source>
	<dc:source>2527-4376</dc:source>
	<dc:source>2087-5517</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://jtrolis.ub.ac.id/index.php/jtrolis/article/view/3604/789</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2025 Journal of Tropical Life Science</dc:rights>
	<dc:rights xml:lang="en">https://creativecommons.org/licenses/by-nc/4.0</dc:rights>
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