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Molecular Identification of Elvers (Anguilla spp.) from River Estuaries in Central Java, Indonesia Using DNA Barcoding Based on mtDNA CO1 Sequences
Corresponding Author(s) : Ratih Ida Adharini
Jurnal Ilmiah Perikanan dan Kelautan,
Vol. 15 No. 1 (2023): JURNAL ILMIAH PERIKANAN DAN KELAUTAN
Abstract
Highlight Research
- The elvers of Anguilla were identified through the morphological and molecular markers
- The result of morphological and molecular identification is different
- The molecular identification helps to confirm the morphological identification
- Based on this study molecular identification of the elvers of Anguilla found in river estuaries of Central Java is Anguilla bicolor bicolor
Abstract
An inventory of the presence and diversity of Anguilla spp. needs to be carried out as a basis for sustainable resource management. Conventional techniques based on morphological characteristics”are often less effective considering the morphological characteristics of Anguilla spp. are very identical and not so many can be observed, especially at the young eel stage. DNA-based molecular identification can be a way to determine diversity and phylogeny for conservation and inventory purposes. This research aimed to determine the diversity and phylogeny of Anguilla spp. obtained at the estuaries of Serayu River in Cilacap, Luk Ulo River in Kebumen, and Jali River in Purworejo in Central Java, Indonesia. A total of 10 samples were taken from each research location were analyzed morphologically, then it is known that there are 4 morphologically different samples at each research location so that a total of 12 samples were taken for molecular analysis. MEGA was used to construct the phylogenetic trees via Neighbour Joining (NJ) algorithms using the Kimura 2-parameter model with uniform rates and obtained by 1000 bootstraps replication. There are four species of Anguilla spp. identified morphologically, namely Anguilla bicolor bicolor, Anguilla bicolor pacifica, Anguilla obscura, and Anguilla australis. The species of Anguilla spp. that is molecularly identified is Anguilla bicolor bicolor with an identity percentage of > 98%. All samples are also known to be related to Anguilla bicolor bicolor identified in other countries.
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- Abdullah, A., Nurilmala, M., Sari, A. S., & Jacoeb, A. M. (2018). Mini-COI barcodes sebagai penanda molekuler untuk ketertelusuran label pangan berbagai produk olahan ikan sidat. Jurnal Pengolahan Hasil Perikanan Indonesia, 21(2):377-384.
- Alter, S. E., Brown, B., & Stiassny, L. J. (2015). Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels. BMC Evolutionary Biology, 15(224):1-12.
- Amrullah, Rosyida, E., Ardiansyah, Hartinah, & Wahidah. (2019). Morphological characters of the giant mottled eel (Anguilla marmorata) from the waters of Sulawesi, Indonesia. AACL Bioflux, 12(5):1799-1805.
- Anggraeni, S. R., Sudarsono, & Soedharma, D. (2008). Karakterisasi genetika rumput laut Eucheuma spp. dari tiga daerah di Indonesia (Kepulauan Seribum Keruak, dan Sumenep). Bionatura Jurnal Ilmu-ilmu Hayati dan Fisik, 10(3):196-208.
- Arai, T. (2016). Biology and ecology of Anguillid Eels. London: CRC Press.
- Arai, T., Taha, H., Mohd-Riduan, M. J., & Mokti, S. S. A. (2020). Molecular and morphological evidence for the identify the giant mottled eel, Anguilla marmorata in Southeast Asia. Tropical Ecology, 61:429-436.
- Arai, T., & Taha, H. (2021). Contrasting patterns of genetic population structure in tropical freshwater eels of genus Anguilla in the Indo-Pacific. Heliyon, 7(e07097):1-10.
- Dekker, W. (2016). Management of the eels is slipping through our hands! Distribute control and orchestra national protection. ICES Journal of Marine Science, 73(10):2442-2452.
- Domingues, L. (2017). PCR methods and protocols. New York: Humana Press.
- Fahmi, M. R. (2015). Konservasi genetik ikan sidat tropis (Anguilla spp.) di perairan Indonesia. Jurnal Penelitian Perikanan Indonesia, 21(1):45-54.
- Fahmi, M. R., Solihin, D. D., Soewardi, K., Pouyaud, L., Shao, Z., & Berrebi, P. (2013). A novel semi-multiplex PCR assay for identification of tropical eels of genus Anguilla in Indonesia water. Fisheries Science, 79:185-191.
- Huyen, K. T., Nghia, V. D., Ngoc, T. N., Dan, T. V., Phu, V. V., Dung, T. Q., & Linh, N. Q. (2020). Using DNA barcodes based on Mitochondrial COI and 16S rRNA genes to identify Anguilla eels in Thua Thien Hue Province, Vietnam. Genetics and Molecular Research, 19(4):1-10.
- Jellyman, D. J. (2021). An enigma: how can freshwater eels (Anguilla spp.) be such a successful genus yet be universally threatened?. Reviews in Fish Biology and Fisheries, 32:701-718.
- Kasai, A., Yamazaki, A., Ahn, H., Yamanaka, H., Kameyama, S., Masuda, R., Azuma, N., Kimura, S., Karaki, T., Kurokawa, Y., & Yamashita, Y. (2021). Distribution of Japanese eel Anguilla japonica revealed by Environmental DNA. Frontiers in Ecology and Evolution, 9:621461.
- Matondo, B. N., & Ovidio, M. (2018). Decreased stock entering the Belgian Meuse is associated with the loss of colonization behavior in yellow-phase European eels. Aquatic Living Resources, 31(7):1-12.
- Nonarfan, A. F., Mokti, S. S. A., Taha, H., Amin, M., Ali, M., & Arai, T. (2021). DNA barcoding of tropical anguilid eel, Anguilla bicolor (Actinopterygii : Anguilliformes), in Indo-Pacific region and notes on its population structure. Zoologia, 38(e59332):1-7.
- Peninal, S., Subramanian, J., Elavarasi, A., & Kalaiselvam, M. (2017). Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters. Genomics Data, 11:81-84.
- Sasmito, D. E. K., Kurniawan, R., & Muhimmah, I. (2014, Desember). Karakteristik primer pada Polymerase Chain Reaction (PCR) untuk Sekuensing DNA: mini review. Paper presented at the Seminar Nasional Informatika Medis V, Universitas Islam Indonesia, Indonesia.
- Silvergrip, A. M. C. (2009). CITES identification guide to freshwater eels (Anguillidae) with focus on the European eel Anguilla anguilla. Sweden: Swedish Environmental Protection Agency.
- Takahashi, S., Takada, S., Yamanaka, H., Masuda, R., & Kasai, A. (2021). Intraspecific genetic variability ad diurnal activity affect environmental DNA detection in Japanese eel. PLoS ONE, 16(9):e0255576.
- Tesch, F. W., & Thorpe, J. E. (2003). The eel (3rd ed.). Oxford: Blackwell Science Ltd.
- Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360:1847-1857.
- Watanabe, S., Minegishi, Y., Yoshinaga, T., Aoyama, J., & Tsukamoto, K. (2004). A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys. Marine Biotechnology, 6:566-574.
- Watanabe, S., Aoyama, J., Miller, M. J., Ishikawa, S., Feunteun, E., & Tsukamoto, K. (2008). Evidence of population structure in the giant mottled eel, Anguilla marmorata, using total number of vertebrae. Copeia, 3:680-688.
- Watanabe, S., Aoyama, J., & Tsukamoto, K. (2009). A new species of freshwater eel Anguilla luzonensis (Teleostei: Anguillidae) from Luzon Island of the Philippines. Fisheries Science, 75:387-392.
- Wibowo, A., Hubert, N., Dahrudin, H., Steinke, D., Suhaimi, R. A., Samuel, Atminarso, D., Anggraeni, D. P., Trismawanti, I., Baumgartner, L. J., & Ning, N. (2021). Assessing temporal pattern and species composition of glass eel (Anguilla spp.) cohort in Sumatra and Java using DNA barcodes. Diversity, 13(5):1-15.
References
Abdullah, A., Nurilmala, M., Sari, A. S., & Jacoeb, A. M. (2018). Mini-COI barcodes sebagai penanda molekuler untuk ketertelusuran label pangan berbagai produk olahan ikan sidat. Jurnal Pengolahan Hasil Perikanan Indonesia, 21(2):377-384.
Alter, S. E., Brown, B., & Stiassny, L. J. (2015). Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels. BMC Evolutionary Biology, 15(224):1-12.
Amrullah, Rosyida, E., Ardiansyah, Hartinah, & Wahidah. (2019). Morphological characters of the giant mottled eel (Anguilla marmorata) from the waters of Sulawesi, Indonesia. AACL Bioflux, 12(5):1799-1805.
Anggraeni, S. R., Sudarsono, & Soedharma, D. (2008). Karakterisasi genetika rumput laut Eucheuma spp. dari tiga daerah di Indonesia (Kepulauan Seribum Keruak, dan Sumenep). Bionatura Jurnal Ilmu-ilmu Hayati dan Fisik, 10(3):196-208.
Arai, T. (2016). Biology and ecology of Anguillid Eels. London: CRC Press.
Arai, T., Taha, H., Mohd-Riduan, M. J., & Mokti, S. S. A. (2020). Molecular and morphological evidence for the identify the giant mottled eel, Anguilla marmorata in Southeast Asia. Tropical Ecology, 61:429-436.
Arai, T., & Taha, H. (2021). Contrasting patterns of genetic population structure in tropical freshwater eels of genus Anguilla in the Indo-Pacific. Heliyon, 7(e07097):1-10.
Dekker, W. (2016). Management of the eels is slipping through our hands! Distribute control and orchestra national protection. ICES Journal of Marine Science, 73(10):2442-2452.
Domingues, L. (2017). PCR methods and protocols. New York: Humana Press.
Fahmi, M. R. (2015). Konservasi genetik ikan sidat tropis (Anguilla spp.) di perairan Indonesia. Jurnal Penelitian Perikanan Indonesia, 21(1):45-54.
Fahmi, M. R., Solihin, D. D., Soewardi, K., Pouyaud, L., Shao, Z., & Berrebi, P. (2013). A novel semi-multiplex PCR assay for identification of tropical eels of genus Anguilla in Indonesia water. Fisheries Science, 79:185-191.
Huyen, K. T., Nghia, V. D., Ngoc, T. N., Dan, T. V., Phu, V. V., Dung, T. Q., & Linh, N. Q. (2020). Using DNA barcodes based on Mitochondrial COI and 16S rRNA genes to identify Anguilla eels in Thua Thien Hue Province, Vietnam. Genetics and Molecular Research, 19(4):1-10.
Jellyman, D. J. (2021). An enigma: how can freshwater eels (Anguilla spp.) be such a successful genus yet be universally threatened?. Reviews in Fish Biology and Fisheries, 32:701-718.
Kasai, A., Yamazaki, A., Ahn, H., Yamanaka, H., Kameyama, S., Masuda, R., Azuma, N., Kimura, S., Karaki, T., Kurokawa, Y., & Yamashita, Y. (2021). Distribution of Japanese eel Anguilla japonica revealed by Environmental DNA. Frontiers in Ecology and Evolution, 9:621461.
Matondo, B. N., & Ovidio, M. (2018). Decreased stock entering the Belgian Meuse is associated with the loss of colonization behavior in yellow-phase European eels. Aquatic Living Resources, 31(7):1-12.
Nonarfan, A. F., Mokti, S. S. A., Taha, H., Amin, M., Ali, M., & Arai, T. (2021). DNA barcoding of tropical anguilid eel, Anguilla bicolor (Actinopterygii : Anguilliformes), in Indo-Pacific region and notes on its population structure. Zoologia, 38(e59332):1-7.
Peninal, S., Subramanian, J., Elavarasi, A., & Kalaiselvam, M. (2017). Genetic identification of marine eels through DNA barcoding from Parangipettai coastal waters. Genomics Data, 11:81-84.
Sasmito, D. E. K., Kurniawan, R., & Muhimmah, I. (2014, Desember). Karakteristik primer pada Polymerase Chain Reaction (PCR) untuk Sekuensing DNA: mini review. Paper presented at the Seminar Nasional Informatika Medis V, Universitas Islam Indonesia, Indonesia.
Silvergrip, A. M. C. (2009). CITES identification guide to freshwater eels (Anguillidae) with focus on the European eel Anguilla anguilla. Sweden: Swedish Environmental Protection Agency.
Takahashi, S., Takada, S., Yamanaka, H., Masuda, R., & Kasai, A. (2021). Intraspecific genetic variability ad diurnal activity affect environmental DNA detection in Japanese eel. PLoS ONE, 16(9):e0255576.
Tesch, F. W., & Thorpe, J. E. (2003). The eel (3rd ed.). Oxford: Blackwell Science Ltd.
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360:1847-1857.
Watanabe, S., Minegishi, Y., Yoshinaga, T., Aoyama, J., & Tsukamoto, K. (2004). A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys. Marine Biotechnology, 6:566-574.
Watanabe, S., Aoyama, J., Miller, M. J., Ishikawa, S., Feunteun, E., & Tsukamoto, K. (2008). Evidence of population structure in the giant mottled eel, Anguilla marmorata, using total number of vertebrae. Copeia, 3:680-688.
Watanabe, S., Aoyama, J., & Tsukamoto, K. (2009). A new species of freshwater eel Anguilla luzonensis (Teleostei: Anguillidae) from Luzon Island of the Philippines. Fisheries Science, 75:387-392.
Wibowo, A., Hubert, N., Dahrudin, H., Steinke, D., Suhaimi, R. A., Samuel, Atminarso, D., Anggraeni, D. P., Trismawanti, I., Baumgartner, L. J., & Ning, N. (2021). Assessing temporal pattern and species composition of glass eel (Anguilla spp.) cohort in Sumatra and Java using DNA barcodes. Diversity, 13(5):1-15.