DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia
Abstract The Apogonidae is estimated to consist of nearly 300 fish species, most of which inhabit coral reef areas. The lack of distinctive body markings and overlapping species distribution makes species assignment challenging. Therefore, this study aimed to delineate species and establish barcod...
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Faculty of Fisheries and Marine Universitas Airlangga
2023-05-01
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| Series: | Jurnal Ilmiah Perikanan dan Kelautan |
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| Online Access: | https://e-journal.unair.ac.id/JIPK/article/view/43336 |
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| author | I Nyoman Giri Putra Putra Gede Surya Indrawan Elok Faiqoh |
| author_facet | I Nyoman Giri Putra Putra Gede Surya Indrawan Elok Faiqoh |
| author_sort | I Nyoman Giri Putra Putra |
| collection | DOAJ |
| description | Abstract
The Apogonidae is estimated to consist of nearly 300 fish species, most of which inhabit coral reef areas. The lack of distinctive body markings and overlapping species distribution makes species assignment challenging. Therefore, this study aimed to delineate species and establish barcoding reference databases of Apogonidae in Gilimanuk Bay (Bali, Indonesia) using the Cytochrome Oxidase I (COI) gene of the mitochondrial DNA. A total of 22 fish tissue samples were extracted with 10% Chelex solution. BLAST analysis was performed and genetic differentiation between species was calculated. The phylogenetic tree was constructed using the Maximum Likelihood method and tree visualization was generated using iTOL V5. The morphology and genetic identification results based on the mitochondrial COI gene revealed eight species of seven genera, and one species was new to GenBank online database. This study was the first-ever addition of COI sequence for Ostorhinchus hartzfeldii into the GenBank database. The average K2P genetic distance within species and K2P distance between genera within the family were 0.60% and 19.10%, respectively. The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species. The phylogenetic tree showed that each sample resided in a distinct cluster, which indicates that DNA barcoding is a reliable and effective approach for species delimitation in Apogonidae fishes.
Highlight Research
• Eight species of cardinalfish in Gilimanuk Bay were delineated using the barcoding method.
• This study provides the first nucleotide sequence for Ostorhinchus hartzfeldii in GenBank online database.
• The phylogenetic tree showed that each sample resided in a distinct cluster, indicating that the barcoding method efficiently differentiated at the species level.
• The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species. |
| format | Article |
| id | doaj-art-b330e30f977946b4bc2a82b4e5965683 |
| institution | Kabale University |
| issn | 2085-5842 2528-0759 |
| language | English |
| publishDate | 2023-05-01 |
| publisher | Faculty of Fisheries and Marine Universitas Airlangga |
| record_format | Article |
| series | Jurnal Ilmiah Perikanan dan Kelautan |
| spelling | doaj-art-b330e30f977946b4bc2a82b4e59656832025-08-20T03:39:19ZengFaculty of Fisheries and Marine Universitas AirlanggaJurnal Ilmiah Perikanan dan Kelautan2085-58422528-07592023-05-0116125526410.20473/jipk.vi.4333641418DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, IndonesiaI Nyoman Giri Putra Putra0https://orcid.org/0000-0002-0773-3923Gede Surya Indrawan1Elok Faiqoh2Department of Marine Science, Faculty of Marine and Fisheries, Udayana University, Badung, Bali, 80361. IndonesiaDepartment of Marine Science, Faculty of Marine and Fisheries, Udayana University, Badung, Bali, 80361. IndonesiaNational Sun Yat-Sen University, Kaohsiung, 804201. TaiwanAbstract The Apogonidae is estimated to consist of nearly 300 fish species, most of which inhabit coral reef areas. The lack of distinctive body markings and overlapping species distribution makes species assignment challenging. Therefore, this study aimed to delineate species and establish barcoding reference databases of Apogonidae in Gilimanuk Bay (Bali, Indonesia) using the Cytochrome Oxidase I (COI) gene of the mitochondrial DNA. A total of 22 fish tissue samples were extracted with 10% Chelex solution. BLAST analysis was performed and genetic differentiation between species was calculated. The phylogenetic tree was constructed using the Maximum Likelihood method and tree visualization was generated using iTOL V5. The morphology and genetic identification results based on the mitochondrial COI gene revealed eight species of seven genera, and one species was new to GenBank online database. This study was the first-ever addition of COI sequence for Ostorhinchus hartzfeldii into the GenBank database. The average K2P genetic distance within species and K2P distance between genera within the family were 0.60% and 19.10%, respectively. The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species. The phylogenetic tree showed that each sample resided in a distinct cluster, which indicates that DNA barcoding is a reliable and effective approach for species delimitation in Apogonidae fishes. Highlight Research • Eight species of cardinalfish in Gilimanuk Bay were delineated using the barcoding method. • This study provides the first nucleotide sequence for Ostorhinchus hartzfeldii in GenBank online database. • The phylogenetic tree showed that each sample resided in a distinct cluster, indicating that the barcoding method efficiently differentiated at the species level. • The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species.https://e-journal.unair.ac.id/JIPK/article/view/43336bali strait banggai cardinalfishcytochrome oxidase iphylogeneticmaximum likelihood |
| spellingShingle | I Nyoman Giri Putra Putra Gede Surya Indrawan Elok Faiqoh DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia Jurnal Ilmiah Perikanan dan Kelautan bali strait banggai cardinalfish cytochrome oxidase i phylogenetic maximum likelihood |
| title | DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia |
| title_full | DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia |
| title_fullStr | DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia |
| title_full_unstemmed | DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia |
| title_short | DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia |
| title_sort | dna barcoding of cardinalfish apogonidae in gilimanuk bay bali indonesia |
| topic | bali strait banggai cardinalfish cytochrome oxidase i phylogenetic maximum likelihood |
| url | https://e-journal.unair.ac.id/JIPK/article/view/43336 |
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