Molecular Identification of Fish Larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia

Agus Nuryanto, Hendro Pramono, Moh Husein Sastranegara


Correct identification of fish larvae from East Plawangan is very difficult to be done due to undefined of their morphology, while correct name is an important information for management of that area as spawning and nersery ground. Therefore, so far no scientific report on what species that utilize East Plawangan as their spawning and nursery ground. Cytochrome c oxidase 1 gene provide a precise tool for correct larvae identification. This study aims to test the accuracy of the cytochrome c oxidase 1 gene on fish larvae identification. The COI gene were amplified and sequenced. The homology of sequences were checked using Basic Local Alignment Search Tool (BLAST). Genetic distances were calculated with the help of MEGA 6 software. Taxonomic tree was reconstructed using neighbor-joining and maximum parsimony methods with 1000 bootstraps repeats. A sum of 24 morphotypes were identified, indicating high diversity of fish that utilize East Plawangan as their spawning and nursery ground. BLAST result showed that seven morphotypes were convincingly identified into species level, while three remaining morphotypes could only be identified at generic level. Taxonomic tree shows clear discrimination among morphotypes. This proved that cytochrome c oxidase 1 gene showed high accuracy on larval species discrimination.


East Plawangan; barcoding; genetic distances; taxonomic tree

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Ardli, E. R. (2007). Spatial and Temporal Dynamic of Mangrove Convertion at the Segara Anakan Cilacap, Java, Indonesia. In: Yuwono, E., Jannerjahn, T., Sastranegara, M.H., Sukardi, P. (eds). Synopsis of Ecological and Socio-economic Aspects of Tropical Coastal Ecosystem with Special Reference to Segara Anakan. Purwokerto: Research Institute Univeristy of Jenderal Soedirman,.pp 11-20.

Barber, P. H., Palumbi, S. R., Erdmand, M. V., & Moosa, M. K. (2002). Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes and consequences. Mol Ecol, 11(4), 659-674.

Bucklin, A., Frost, B. W., Bradford-Grieve, J., Allen, L. D., & Copley, N. J. (2003). Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae. Mar Biol, 142(2), 333-343.

Dor, L. (2012). Establishment of genetic markers for spawning the white grouper (Epinephelus aeneus). Master Thesis. Jerusalem: Faculty of Agriculture, Food, and Environment, the Hebrew University of Jerusalem.

Folmer, O., Black, M., Lutz, R., & Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit i from metazoan invertebrates. Mol Mar Biol Biotechnol, 3(5), 294-299.

Frankham, R. (2003). Genetics and conservation. C.R. Biologes, 326, 22-29.

Froese, R., & Pauly, D. (2016). FishBase. World Wide Web electronic Publication., version (06/2016).

Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nuc Acids Symp Ser, 41, 95-98.

Hebert, P. D. N., Ratnasingham, R., & deWaard, J. R. (2003a). Barcoding animal life: cytochrome c oxidase subunit i divergences among closely related species. Proc. R. Soc. Lond. B, 270, S96-99

Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003b). Biological identification through dna barcodes. Proc. R. Soc. Lond. B 270, 313-321

Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004). Identification of birds through dna barcodes. PloS Biol, 2, 1657-1663

Ko, H. L., Wang, Y. T., Chiu, T. S., Lee, M. A., Leu, M. Y., Chang, K. Z. Chen, W. Y., & Shao, K. T. (2013). Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. Plos One, 8(1), 253451.

Kumar, S., Nei, M., Dudley, J., & Tamura, K. (2008). MEGA: a biologist-centric software for evolutionary analysis of dna and protein sequences. Briefings in Bioinformatics, 9(4), 299-306.

Kurniawaty, N., Hidayat, P. & Rauf, A. (2016). Characterization of Three Species of Thrips on Banyan, Nutmeg, and Marine Seruni Plants Based on COI Gene. Biosaintifika: Journal of Biology & Biology Education, 8(2), 185-192.

Leis, J. M. & Carson-Ewart, B. M. (2004). The Larvae of Indo-Pacific Coastal Fishes. 2nd edition, Leiden. Boston: Brill.

Manez, K. S. (2010). Javas forgoten pearls: the history and disappearance of pearl fishing in the Segara Anakan Lagoon, South Java, Indonesia. J Hist Geograp, 36(4), 367-376.

Naamin, N. (1991). The Ecological and Economic Roles of Segara Anakan,Indonesia, as Nursery Ground of Shrimps. In: Chou, L.M., Chua, T.E., Khoo, H.W. Lim, P.E., Paw, J.N., Silvestre, G.T., Valencia, M.J., White, A.T., &Wong, P.K. (eds). Towards an Integrated Management of Tropical Coastal Resources. ICLARM Conf Proc. 22, 119-130.

Nuryanto, A. & Pramono, H. (2015). DNA barcoding and phylogeography of groupers in Spermonde Archipelago South Sulawesi. International Research Collaboration Report. Purwokerto: Lembaga Penelitian dan Pengabdian Kepada Masyarakat-Unsoed.

Nuryanto, A., Solihin, D. D., Soedharma, D., & Blohm, D. (2007). Molecular phylogeny of giant clams based on mitochondrial dna cytochrome c oxidase 1 gene. HAYATI Journal of Biosciences, 14(4), 162-166.

Pegg G. G., Sinclair, B., Briskey, L., & Aspden, W. J. (2006). MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia. Scientia Marina, 70(S2), 7-12.

Romimohtarto, K., Hutagalung, H., & Razak, H. (1991). Water Quality of Segara Anakan-Cilacap (Central Java, Indonesia) with a Note on Lagoon Fishery. In: Chou, L.M., Chua, T.E., Khoo, H.W. Lim, P.E., Paw,J.N., Silvestre, G.T., Valencia, M.J., White, A.T., Wong, P.K. (eds). Towards an Integrated Management of Tropical Coastal Resources. ICLARM Conf Proc. 22, 131-141.

Sachithanandam, V., Mohan, P. M., Muruganandam, N., Chaaithanya, I. K., Dhivya, P., & Baskaaran, R. (2012). DNA barcoding, phylogenetic study of Epinephelus spp. from Andaman Coastal Region, India. Indian Journal of Geo-Marine Sciences, 41(4), 203-211.

Shao, K. T., Chen, K. C., & Wu, J. H. (2002). Identification of marine fish eggs in Taiwan using light microscope, scanning electron microscope and mtDNA sequencing. Mar Freshw Res, 53(2), 355-365.

Susanto A. H., Nuryanto, A., & Soedibja, P. H. T. (2011). Phylogeography and genetic diversity of humpback grouper Cromileptes lativelis based on cytochrome c oxidase I. Jurnal Natur Indonesia, 14(1), 47-51

Thirumaraiselvi, R., Das, S., Ramanadevi, V., & Thangaraj, M. (2015). MtDNA barcode identification of fisnfish larvae from Vellar Estuary, Tamilnadu, India. Notulae Scientia Biologicae, 7(1), 16-19.

Thompson, J. G., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680.

Victor, B. C., Hanner, R., Shivji, M., Hyde, J., & Caldow, C. (2009). Identification of larval and juvenile stages of the cubera snapper, Lutjanus cyanopterus, using DNA barcoding. ZooTaxa, 2215(2), 24-36.

von der Heyden, S., Berger, M., Toonen, R. J., van Herwerden, L., Juinio-Menez, M. A., Ravago-Gotanco, R., Fauvelot, C., & Bernardi, G. (2014). The application of genetics to marine management and consrvation: examples from the Indo-Pacific. Bull Mar Sci, 90(1), 123-158.

Ward, R. D., Holmes, B. H., White, W. T., & Last, P. R. (2008a). DNA barcoding Australian Chondrichthyans: results and potential uses in conservation. Marine and Freshwater Research, 59(1), 57-71.

Ward, R. D., Holmes, B. H., & Yearsley, G. K. (2008b). DNA barcoding reveals a likely second species of Asian seabass (Barramundi) (Lates calcarifer). J Fish Biol, 72(2), 458-463

Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA barcoding Australias fish species. Phil Trans R Soc B, 360(1462), 1847-1857.

White, A. T., Martosubroto, P., & Sadorra, M. S. M. (1989). The Coastal Environment Profile of Segara Anakan-Cilacap, South Java, Indonesia. ICLARM. Association of Southeast Asian Nations. United States Coastal Resources Management Project. Techn Publ Ser, 4, 81.



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