DNA barcoding of Crustacean larvae in the eastern areas of Segara Anakan Cilacap, Central Java Indonesia
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Abstract. Kusbiyanto, Bhagawati D, Nuryanto A. 2020. DNA barcoding of crustacean larvae in Segara Anakan, Cilacap, Central Java, Indonesia using cytochrome c oxidase gene. Biodiversitas 21: 4878-4887. Species-level identification of crustacean larvae is challenging due to morphological constraints. DNA barcoding offers a precise method to solve the problems. That method has never been applied to crustacean larvae from the eastern of Segara Anakan, Cilacap, Central Java, Indonesia. This study aims to identify crustacean larvae in the eastern of Segara Anakan using the cytochrome c oxidase subunit I (COI) gene as a barcode marker. Larvae morphotypes were identified under a binocular microscope. The COI gene was sequenced from one individual of each morphotype. Microscopic observation placed the samples into 15 morphotypes. DNA barcoding placed twelve morphotypes as Crustacea with sequence homologies from 72.21% to 99.21%. Intra-species genetic divergences between samples and reference species ranged between 0.9% and 31.9%, while genetic distance ranged from 0.0% to 17.80%. Intra-species genetic divergences ranged between 0.00% and 3.9%, while genetic distance ranged from 0.00% to 3.8%. The phylogenetic tree proved the monophyly between samples and reference species and showed clear separation among species. All parameters proved that nine morphotypes were identified into species level and were counted for five species. Three morphotypes were identified into the genus level and were counted for three genera. Eight species of crustacean larvae were successfully identified using the cytochrome c oxidase subunit 1 gene.
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References
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Yoshida Masa-aki, Tsuneki K, Furuya H. 2006. Phylogeny of selected Sepiidae (Mollusca, Cephalopoda) based on 12S, 16S, and COI sequences, with comments on the taxonomic reliability of several morphological characters. Zoological Science 23: 341-351
Zalindri M, Sastranegara MH. 2015. Community structure of intertidal crab in degraded mangrove in Segara Anakan Cilacap. Biosfera 32(3): 154-161. [Indonesian]
Akbar PP, Solichin A, Saputra SW. 2013. Analysis of length-weight relationship and condition factor of rebon shrimp (Acetes japonicas) in Cilacap of Center Java. Journal of Management of Aquatic Resources 2(3): 161-169. [Indonesian]
Ardli ER. 2007. Spatial and Temporal Dynamic of Mangrove Conversion at the Segara Anakan Cilacap, Java, Indonesia. In: Yuwono E, Jannerjahn T, Sastranegara MH, Sukardi P (eds) Synopsis of Ecological and Socio-economic Aspects of Tropical Coastal Ecosystem with SpecialReference to Segara Anakan. Research Institute University of Jenderal Soedirman, Purwokerto.
Asmara H, Riani E, Susanto A. 2011. Analysis of some reproductive aspects of mangrove crab (Scylla serrata) in Segara Anakan waters, Cilacap Regency, Central Java. Jurnal Matematika, Saint dan Teknologi 12(1): 30-36. [Indonesian]
Bekker EI, Karabanov DP, Galimov YR, Kotov AA. 2018. DNA barcoding reveals high cryptic diversity in the North Eurasian Moina species (Crustacea: Cladocera). PloS one 11(8): e0161737.
Bhagawati D, Winarni ET, Nuryanto A. 2020. Molecular barcoding reveals the existence of mole crabs Emerita emeritus in North Coast of Central Java. Biosaintifika 12(1): 104-110.
Bilgin R, Utkan MA, Kalkan E, Karhan SU, Bekbolet M. 2015. DNA barcoding of twelve shrimp (Crustacea: Decapoda) from Turkish sea reveals cryptic diversity. Mediterranean Marine Science 16(1): 36-45.
Camacho AI, Dorda BA, Rey I. 2011. Identifying cryptic speciation across groundwater populations: first COI sequences of Bathynellidae (Crustacea, Syncarida). Graellsia 67(1): 7-12.
da Silva JM, Creer S, dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR. 2011. Systematic and Evolutionary Insights Derived from
mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca). PLoSONE 6(5): e19449.
Deli T, Kalkan E, Karha SU, Uzunova S, Keikhosravi A, Bilgin R, Schubart CD. 2018. Parapatric divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean. BMC Evolutionary Biology 18: 53. https://doi.org/10.1186/s12862-018-1167-4
Djuwito, Saputra SW, Widyaningtiwi WA. 2013. Ecological aspects of mantis shrimp (Oratosquilla oratoria De Haan, 1844) in Cilacap water, Central Java. Journal of Management of Aquatic Resources 2(3): 56-64. [Indonesian]
Hall TA. 2005. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identification through DNA barcodes. Proceeding of Royal Society London B 270: 313-321
Jeffery NW, Elias-Guttierrez M, Adamowicz SJ. 2011. Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada. PLoS one 6(5): e18364
Karanovic I. 2015. Barcoding of ancient lake Ostracods (Crustacea) reveals cryptic speciation with extremely low distances. PLoS one 10(3): e0121133.
Ko HL, Wang YT, Chiu TS, Lee MA, Leu MY, Chang KZ, Chen WY, Shao KT. 2013. Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS ONE, 8(1), 253451.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018 MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35:1547-1549
Manez KS. 2010. Java’s forgotten pearls: The history and disappearance of pearl fishing in the Segara Anakan Lagoon, South Java, Indonesia. Journal of Historical Geography 36: 367-376.
Nordhaus I, Hadipudjana FA, Jansen R, Pamungkas J. 2009. Spatio-temporal variation of microbenthic communities in the mangrove-fringed Segara Anakanlagoon Indonesia, affected by anthropogenic activities. Regional Environmental Change 9: 291-313
Nuryanto A, Pramono H, Sastranegara MH. 2017. Molecular Identification of Fish Larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia. Biosaintifika 9(1): 33-40.
Nuryanto A, Amalia G, Khairani D, Pramono H, Bhagawati D. 2018. Molecular characterization four giant gourami strains from Java dan Sumatra. Biodiversitas 19(2): 528-539.
Nuryanto A, Komalawati N, Sugiharto. 2019. Genetic diversity assessment of Hemibagrus nemurus from rivers in Java Island, Indonesia using COI gene. Biodiversitas 20 (9): 2707-2717.
Pegg GG, Sinclair B, Briskey L, Aspden WJ. 2006. MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia. Scientia Marina 70S2: 7-12.
Pereira LHG, Hanner R, Foresti F, Oliveira C. 2013. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genetics 12:20. 1471-2156/14/20
Palomares MLD, Pauly D. 2019. Editors. SeaLifeBase. World Wide Web Electronic Publication. www.sealifebase.org. Version 12,2019. Accessed 2020-08-11.
Pratiwi R, Sukardjo S. 2018. Effect of Rainfall on the Population of Shrimps Penaeus monodon Fabricius in Segara Anakan Lagoo, Central Java, Indonesia. Biotropia 25(3): 156-169.
Raupach MJ, Radulovici AE. 2015. Looking back on a decade barcoding crustaceans. Zookeys 539: 53-81.
Redjeki S, Arif M, Hartati R, Pinandita LK. 2017. Density and distribution of crab (Brachiura) in mangrove forest ecosystem of Segara Anakan Segara Anakan Cilacap. Jurnal Kelautan Tropis 20(2): 131-139. [Indonesia]
Riehl T, Brenke N, Brix S, Driskell A, Kaiser S, Brandt A. 2014. Field and laboratory methods for DNA studies on deep-sea isopod crustaceans. Polish Polar Research 35(22): 203-224.
Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Osins SE, Sanchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34(12): 3299-3302.
Saputra SW. 2010. Study on biological aspects of shrimp Leptocarpus potamiscus Segara Anakan lagoon Cilacap Central Java. Pena Akuatika 1(1): 76-84. [Indonesia]
Tang RWK, Yau C, Ng W-C. 2010. Identification of stomatopod larvae (Crustacea: Stomatopoda) from Hong Kong waters using DNA barcodes. Molecular Ecology Resources 10: 439-448.
Thompson, J.G., Higgins, D.G., and 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: 4673–4680.
Wagiyo, K., Damora, A., dan Pane, A.R.P. 2018. Aspek Biologi, Dinamika Populasi, dan Kepadatan Stok Udang Jerbung (Penaeus merguiensis de Man, 1888) di Habitat Asuahn Estuaria Segara Anakan, Cilacap. Jurnal Penelitian Perikanan Indonesia 24(2): 127-136.
Weis M, Macher JN, Seefeldt MA, Leese F. 2014. Molecular evidence for further overlooked species within the Gammarus fossarum complex (Crustacea: Amphipoda). Hydrobiologia 721: 165-184.
Widianingsih, Nuraini, R.A.T., Hartati, R., Redjeki, S., Riniatsih, I., Andanar, C.E., Endrawati, H., dan Mahendrajaya, R.T. 2019. Morfometri dan Pertumbuhan Scylla serrata (Filum: Arthropoda, Famili: Portunidae) di Desa Panikel, Segara Anakan, Cilacap. Jurnal Kelautan Tropis 22(1): 57-62.
WoRMS Editorial Board. 2020. World Register of Marine Species. Available from http://www.marinespecies.org at VLIZ. Accessed 2020-08-11. DOI:10.14284/170
Yoshida Masa-aki, Tsuneki K, Furuya H. 2006. Phylogeny of selected Sepiidae (Mollusca, Cephalopoda) based on 12S, 16S, and COI sequences, with comments on the taxonomic reliability of several morphological characters. Zoological Science 23: 341-351
Zalindri M, Sastranegara MH. 2015. Community structure of intertidal crab in degraded mangrove in Segara Anakan Cilacap. Biosfera 32(3): 154-161. [Indonesian]
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