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Type :article
Subject :QH301 Biology
ISSN :2462-2052
Main Author :Kamarudin Kamarul Rahim, Mohamed Rehan Maryam, Mohd Noor Hanina, Ramly Nur Zazarina, Mohamed Rehan ‘Aisyah,
Title :16S rRNA barcoding technique for species identification of processed sea cucumbers from selected Malaysian markets (IR)
Place of Production :Universiti Pendidikan Sultan Idris
Year of Publication :2016
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In food industry, wide-ranging processing of sea cucumbers (Phylum Echinodermata: Class Holothuroidea) including gutting, boiling, roasting, and subsequent preservation procedures are frequently needed prior to marketing. These processes cause body deformation of the sea cucumbers, thus leading to difficulties in species identification and confirmation of the processed sea cucumbers or beche-de-mer. Furthermore, beche-de-mer products in Malaysian markets are often unlabelled or mislabelled. Economic fraud, health hazards, and illegal trade of protected species are the potential major consequences of the issues. Therefore, a reliable, reproducible, and rapid technique for species identification is required. For that reason, this study was conducted to determine species identity of 25 beche-de-mer specimens that were not tagged with species details from four selected Malaysian markets. Five reference samples were also included in the analyses consisting of fresh samples that were morphologically identified as Stichopus horrens and Holothuria (Mertensiothuria) leucospilota from Pangkor Island, Perak, Malaysia. Phylogenetic analyses of 30 partial sequences of non-protein-coding 16S mitochondrial ribosomal RNA (rRNA) gene using five main methods i.e. Neighbour-Joining (NJ), Maximum Likelihood (ML), Minimum Evolution (ME), Unweighted Pair Group Method with Arithmetic Mean (UPGMA), and Maximum Parsimony (MP) showed the presence of two main clusters of the beche-demer specimens: Stichopodidae (gamat family) and Holothuriidae (timun laut family). The beche-de-mer specimens of S. horrens, Stichopus herrmanni, and Thelenota anax were the three gamat species that clustered under the family Stichopodidae. Meanwhile, the beche-de-mer specimens of H. leucospilota, Holothuria (Halodeima) edulis, Holothuria (Metriatyla) scabra, and H. scabra var. versicolor were the four timun laut species that clustered under the family Holothuriidae. In fact, the outcomes of this study suggested the potential of 16S mitochondrial rRNA gene sequencing technique to be used by the enforcement agencies in monitoring and overcoming the issues of species substitution and product mislabeling of beche-de-mer products in Malaysian markets.

1. Amos, B. and Hoelzel, A. R. (1992). Application of Molecular Genetic Techniques to The Conservation of small populations. Biological Conservation 61: 133-144. 2. Bartlett, S. E. and Davidson, W. S. (1992). FINS (forensically informative nucleotide sequencing): a procedure for identifying the animal origin of biological specimens. Bio Tech 12(3): 408–11. 3. Choo, P. S. (2008). Population status, fisheries and trade of sea cucumbers in Asia. In Toral-Granda V., Lovatelli A. and Vasconcellos M. (ed). Sea cucumbers. A global review of fisheries and trade. Pp. 81-118. FAO Fisheries and Aquaculture Technical Paper. No. 516. 4. Clouse, R., Janies, D. and Kerr, A. M. (2005). Resurrection of Bohadschia bivittata from B. Marmorata (Holothuroidea: Holothuriidae) based on behavioral, morphological, and mitochondrial DNA evidence. Zoological 108: 27-39. 5. Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791. 6. Hashim, R. B. (1993). Sumber Makanan Persisiran Laut Sabah. Kuala Lumpur: Dewan Bahasa dan Pustaka. 7. Hashim, R. B. (2011). Timun Laut Warisan Malaysia. Kuala Lumpur: Research Management Centre, International Islamic University Malaysia. 8. Kamarudin, K. R., Rehan, A. M., Hashim, R. and Usup, G. (2010). An Update on Diversity of Sea Cucumber (Echinodermata: Holothuroidea) in Malaysia. Malayan Nature Journal 62(3): 315- 334. 9. Kamarudin, K. R., Rehan, A. M., Hashim, R., Usup, G., Ahmad, H. F., Anua, M. H. and Idris, M. Y. (2011). Molecular Phylogeny of Holothuria (Mertensiothuria) leucospilota (Brandt 1835) as Inferred from Cytochrome C Oxidase I Mitochondrial DNA Gene Sequences. Sains Malaysiana 40 (2): 125-133. 10. Kamarudin, K. R., Rehan, A. M., Mohd Noor, H., Ramly, N. Z. and Mohamed Rehan, M. (2015a). Molecular Species Identification of Processed Sea Cucumbers from Selected Malaysian Markets Using COI MtDNA Gene. In proceeding of International Conference on Biodiversity and Conservation 2015 (ICBC 2015) – “Sustaining Biodiversity for Sustainable Future”, organised by Centre for Biodiversity and Conservation, Faculty of Science and Mathematics, Sultan Idris Education University (UPSI), Tanjong Malim, Perak Darul Ridzuan, Malaysia, 26-28 May 2015, Convention Hall, E-Learning Building, Sultan Idris Education University (UPSI), Tanjong Malim, Perak Darul Ridzuan, Malaysia. Pp. 5-28. 11. Kamarudin, K. R., Usup, G., Hashim, R. and Mohamed Rehan, M. (2015b). Sea Cucumber (Echinodermata: Holothuroidea) Species Richness at Selected Localities in Malaysia. Pertanika Journal of Tropical Agricultural Science 38(1): 7–32. 12. Kerr, A. M., Janies, D. A., Clouse, R. M., Samyn, Y., Kuszak, J. and Kim, J. (2005). Molecular Phylogeny of Coral-Reef Sea Cucumbers (Holothuriidae: Aspidochirotida) Based on 16S Mitochondrial Ribosomal DNA Sequence. Marine Biotechnology 7: 53-60. 13. Lukman, A. L., Nordin, N. F. H. and Kamarudin, K. R. (2014). Microbial Population in the Coelomic Fluid of Stichopus chloronotus and Holothuria (Mertensiothuria) leucospilota collected from Malaysian waters. Sains Malaysiana 43(7): 1013–1021. 14. Nabholz, B., Mauffrey, J. F., Bazin, E., Galtier, N. and Glemin, S. (2008). Determination of mitochondrial genetic diversity in mammals. Genetics 178(1): 351-361. 15. Nei, M. and Kumar, S. (2000). Molecular Evolution and Phylogenetics. New York: Oxford University Press. 16. Purcell, S. W., Samyn, Y. and Conand, C. (2012). Commercially important sea cucumbers of the world. FAO Species Catalogue for Fishery Purposes No. 6. Rome: Food and Agriculture Organization of The United Nations (FAO). 17. Rasmussen, R. S. and Morrissey, M. T. (2008). DNA-Based Methods for the Identification of Commercial Fish and Seafood Species. Comprehensive Reviews in Food Science and Food Safety 7: 280-295. 18. Rzhetsky, A. and Nei, M. (1992). A simple method for estimating and testing minimum evolution trees. Molecular Biology and Evolution 9: 945-967. 19. Saitou, N. and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425. 20. Sneath, P. H. A. and Sokal, R. R. (1973). Numerical Taxonomy. San Francisco: Freeman. Tamura, K. and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10: 512-526. 21. Tamura, K., Nei, M. and Kumar, S. (2004). Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101:11030-11035. 22. Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729. 23. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G. (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by the quality analysis tools. Nucleic Acids Research 24: 4876-4882.

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