Advancing traceability using DNA sequence on seafood product: fraudulence in shrimp crackers
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Abstract. Nurilmala M, Atjitama Y, Jacob AM, Indarwati AR, Nugraha R. 2020. Advancing traceability using DNA sequence on seafood product: fraudulence in shrimp crackers. Biodiversitas 21: 5650-5656. Shrimp crackers are snacks made from starch with the addition of shrimp and other ingredients. Authentication of shrimp crackers becomes a quality control method in line with its traceability since the morphological characters are not recognized in those products. The failure of the authentication will lead to adulteration of shrimp products. The study aimed to design shrimp-specific polymerase chain reaction (PCR) primers by and used them to authenticate shrimp cracker products to assure their traceability. The primers were designed from cytochrome oxidase subunit I (COI) gene with a GC content of 50% and a melting temperature of 57 °C. The amplicon had a length of 613 bp. Fourteen shrimp crackers having DNA concentrations 0.3 to 8.1 ng/µL were evaluated. Eight out of fourteen DNA samples were successfully amplified using the specific primer and could be visualized on the agarose gel at 500-750 bp. Those DNA samples were identified belonging to shrimp species, namely Litopenaeus vannamei, Metapenaeus ensis, and Fenneropenaeus merguiensis with 95% to 100% identity. Meanwhile, the other six DNA samples underwent PCR using universal primers. One sample was amplified and identified as fish (Sphyraena flavicauda). These results indicate illegal substitution of shrimp using unidentified species occurred in shrimp crackers.
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References
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Barcaccia G, Lucchin M, Cassandro M. 2015. DNA barcoding as a molecular tool to track down mislabeling and food piracy. Diversity 8:1-16.
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Brodin J, Mohan K, Gayathri A, Will F, Peter H, Cheryl G, Lance G, Bette K, Thomas T. 2013. A multiple-alignment based primer design algorithm for genetically highly variable DNA targets. BMC Bioinformatics 14: 255.
Carvalho CD, Palhares RM, Drummond MG, Frigo TB. 2015. DNA barcoding identification of commercialized seafood in South Brazil: a governmental regulatory forensic program. Food Control 50:784-788.
Corrado F, Cutarelli A, Criscuolo D, Roma AD, Cecere B, Simonetti D, Galiero G, Coccia E, Viola C, Varrichio E, Paolucci M. 2016. Identification of fraud in trade in processed fish products by DNA analysis. Imekofoods 2: 1-4.
Destrasia RF. 2012. Comparative study of shrimp head prawn manufacture with composite flour. Food Science and Culinary Education Journal 1: 1-5.
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Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3:294-299.
Hebert PDN, Cywinska A, Ball SL. 2003. Biological identification through DNA barcodes. The Royal Society 270:313-321.
[KKP] Kementerian Kelautan dan Perikanan. 2018. Kelautan dan Perikanan dalam
Angka Tahun 2018. Kementerian Kelautan dan Perikanan. Jakarta. [Indonesian]
Klossa-Kilia E, Papasotiropoulos V, Kilias G, Alahiotis S. 2002. Authentication of Messolongi (Greece) fish roe using PCR-RFLP analysis of 16s rRNA mtDNA segment. Food Control 227: 680-685.
Krauthammer M, Rzhetsky A, Morozov P, Friedman C. 2000. Using BLAST for identifying gene and protein names in journal articles. Gene 259: 245-252.
Leeuwen SP, van Velzen MJ, Swart CP, van der Veen I, Traag WA, de Boer J. 2009. Halogenated contaminants in farmed salmon, trout, tilapia, pangasius, and shrimp. Environmental Science and Technology 43:4009-4015.
Lockley AK, Bradsley RG. 2000. DNA-based method for food authentication. Trends in Food Science and Technology 11:67-77.
Lin WF, Hwang DF. 2008. A multiplex of PCR assay for species identification of raw and cooked Bonito. Food Control 19(9):879-855.
Maulid DY. 2016. Detection of mackerel (Scomberomorus sp.)and its processed products using DNA barcoding. Graduate School of IPB University. Bogor. [Indonesian]
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Maulid DY, Nurilmala M. 2015. DNA barcoding for authentication of mackerel fish products (Scomberomorus sp.). Jurnal Akuatika 6: 154-160.
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Nurilmala M, Ochiai Y. 2016. Molecular characterization of southern bluefin tuna myoglobin (Thunnus maccoyii). Fish Physiology and Biochemistry 42(5): 1407-1416
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Quan J, Zhuang Z, Deng J, Dai J, Zhang Y. 2004. Phylogenetic relaionship of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochemical Genetics 42(9/10):331-345. 14
Rajkumar G, Bhavan PS, Udayasuriyan R, Vadilagan. 2015. Molecular identification of shrimp species, Penaeus semisulcatus, Metepenaeus dobsoni, Metapenaeus brevicornis, Fenneropenaeus indicus, Parapenaeopsis sylifera and Solenocera crassicornis inhabiting in the coromandel coast (Tamil Nadu, India) using MT-COI gene. Internasional Journal of Fisheries and Aquatic Studies 2(4):96-106
Sambrook J, Russell DW. 2001. Molecular Cloning : a Laboratory Manual 3rd Edition. Cold Spring Harbor [New York]
Scarano D, Rao R. 2014. DNA markers for food products authentication. Diversity 6:579-596
Shokralla S, Hellberg RS, Handy SM, King I, Hajibabaei M. 2015. A DNA minibarcoding system for authentication of processed fish product. Science Reports 5:1-11
Smith PJ, McVeagh SM, Steinke D. 2007. DNA barcoding for the identification of smoked fish. Journal of Fish Biology 72:464-471
Stevanofa P, Taseva M, Georgieva T, Gotcheva V, Angelov A. 2013. A modified CTAB method for DNA extraction from soybean and meat products. Biotechnology & Biotechnological Equipment 27(3):3803-3810
Tamura K, Glen S, Daniel P, Alan F, Sudhir K. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 33(2):11-25
Udayasuriyan R, Bhavan PS, Vadivalagan C, Rajkumar G. 2015. Efficiency of different COI markers in DNA barcoding of freshwater prawn species. Journal of Entomology and Zoology Studies 3(3):98-110
Voloch CM, Freire PR, Russo CAM. 2005. Molecular phylogeny of penaeid shrimp inferred from two mitochondrial markers. Genetics and Molecular Research 4(4):668-678
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of The Royal Society B 360:1847-1857
Westermeier R. 2005. Electrophoresis in Preactice. Weinheim (GE): Wiley-VCH
Wulansari N, Nurilmala M, Nurjanah. 2015. Deteksi ikan tuna dan produk olahannya berbasis protein dan DNA barcoding. Jurnal Pengolahan Hasil Perikanan Indonesia. 18(2):119-127
Xiong X, Huang M, Yuang F, Lu L, Xiong X. 2019. Development and validation of a fast DNA extraction protocol for fish product. Food Analitical Methods 10: 1-11. DOI: 10.1007/s12161-019-01554-z.
Yakovchuk P, Ekaterina P, Maxim DF-K. 2006. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acid Research 34(2):564-574
Zein MSA, Sulandari S. 2009. Investigasi asal-usul ayam Indonesia menggunakan sekuen hypervariable-1 d-loop mtDNA. Veteriner Maret 10(1):41-49
Zella AP. 2013. Karakterisasi genom mitokondria ikan pada gen cytochrome oxydase subunit 1 (COI) dan cytochrome b (CytB). [Skripsi]. IPB University, Bogor. [Indonesian]
Zhang Q, Cheng Q, Guan W. 2009. Mitochondrial COI gene sequence variation and taxonomic status of three Macrobrachium species. Zoological Research 30(6):613-619
Zhou J, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology 62(2):316-322
Barcaccia G, Lucchin M, Cassandro M. 2015. DNA barcoding as a molecular tool to track down mislabeling and food piracy. Diversity 8:1-16.
Borah P. 2011. Primer designing for PCR. Science Vision 11: 134-136.
Brodin J, Mohan K, Gayathri A, Will F, Peter H, Cheryl G, Lance G, Bette K, Thomas T. 2013. A multiple-alignment based primer design algorithm for genetically highly variable DNA targets. BMC Bioinformatics 14: 255.
Carvalho CD, Palhares RM, Drummond MG, Frigo TB. 2015. DNA barcoding identification of commercialized seafood in South Brazil: a governmental regulatory forensic program. Food Control 50:784-788.
Corrado F, Cutarelli A, Criscuolo D, Roma AD, Cecere B, Simonetti D, Galiero G, Coccia E, Viola C, Varrichio E, Paolucci M. 2016. Identification of fraud in trade in processed fish products by DNA analysis. Imekofoods 2: 1-4.
Destrasia RF. 2012. Comparative study of shrimp head prawn manufacture with composite flour. Food Science and Culinary Education Journal 1: 1-5.
Dieffenbach M, Lowe TMJ, Dveksler GS. 1993. General Concept for PCR Primer Design. Cold Spring Harbor Laboratory Press: New York.
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3:294-299.
Hebert PDN, Cywinska A, Ball SL. 2003. Biological identification through DNA barcodes. The Royal Society 270:313-321.
[KKP] Kementerian Kelautan dan Perikanan. 2018. Kelautan dan Perikanan dalam
Angka Tahun 2018. Kementerian Kelautan dan Perikanan. Jakarta. [Indonesian]
Klossa-Kilia E, Papasotiropoulos V, Kilias G, Alahiotis S. 2002. Authentication of Messolongi (Greece) fish roe using PCR-RFLP analysis of 16s rRNA mtDNA segment. Food Control 227: 680-685.
Krauthammer M, Rzhetsky A, Morozov P, Friedman C. 2000. Using BLAST for identifying gene and protein names in journal articles. Gene 259: 245-252.
Leeuwen SP, van Velzen MJ, Swart CP, van der Veen I, Traag WA, de Boer J. 2009. Halogenated contaminants in farmed salmon, trout, tilapia, pangasius, and shrimp. Environmental Science and Technology 43:4009-4015.
Lockley AK, Bradsley RG. 2000. DNA-based method for food authentication. Trends in Food Science and Technology 11:67-77.
Lin WF, Hwang DF. 2008. A multiplex of PCR assay for species identification of raw and cooked Bonito. Food Control 19(9):879-855.
Maulid DY. 2016. Detection of mackerel (Scomberomorus sp.)and its processed products using DNA barcoding. Graduate School of IPB University. Bogor. [Indonesian]
Maulid DY, Nurilmala M, Nurjanah, Maddupa H. 2016. Characteristics of molecular cytochrome b for DNA barcoding of mackerel fish (Scomberomorus sp.). Jurnal Pengolahan Hasil Perikanan Indonesia 19: 9-16.
Maulid DY, Nurilmala M. 2015. DNA barcoding for authentication of mackerel fish products (Scomberomorus sp.). Jurnal Akuatika 6: 154-160.
Nuraini H. 2004. Pengembangan sekuen porcine repetitive Element-1 (PRE-1) sebagai penanda molekuler untuk mendeteksi material babi pada produk daging olahan. [Thesis]. IPB University, Bogor. [Indonesian]
Nurilmala M, Ochiai Y. 2016. Molecular characterization of southern bluefin tuna myoglobin (Thunnus maccoyii). Fish Physiology and Biochemistry 42(5): 1407-1416
Nurilmala M, Widyastuti U, Kusuma WA, Nurjanah, Wulansari N, Widyatuti Y. 2016. DNA barcoding for identification of processed tuna fish in Indonesian market. Jurnal Teknologi. 78(4-2):115-118
Olson ND, Morrow BJ. 2012. DNA extract characterization process for microbial detection methods development and validation. Olson and Morrow BMC Research Notes 5:668
Page RDM, Holmes EC. 1998. Molecular Evolution: A Phylogenetic Approach. Blackwell Science [Inggris]
Popa OP, Murariu D, Popa LO. 2007. Comparison of four DNA extraction methods from invasive freshwater bivalve species in Romanian Fauna. Grigore Entipa. L: 527-539
Quan J, Zhuang Z, Deng J, Dai J, Zhang Y. 2004. Phylogenetic relaionship of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochemical Genetics 42(9/10):331-345. 14
Rajkumar G, Bhavan PS, Udayasuriyan R, Vadilagan. 2015. Molecular identification of shrimp species, Penaeus semisulcatus, Metepenaeus dobsoni, Metapenaeus brevicornis, Fenneropenaeus indicus, Parapenaeopsis sylifera and Solenocera crassicornis inhabiting in the coromandel coast (Tamil Nadu, India) using MT-COI gene. Internasional Journal of Fisheries and Aquatic Studies 2(4):96-106
Sambrook J, Russell DW. 2001. Molecular Cloning : a Laboratory Manual 3rd Edition. Cold Spring Harbor [New York]
Scarano D, Rao R. 2014. DNA markers for food products authentication. Diversity 6:579-596
Shokralla S, Hellberg RS, Handy SM, King I, Hajibabaei M. 2015. A DNA minibarcoding system for authentication of processed fish product. Science Reports 5:1-11
Smith PJ, McVeagh SM, Steinke D. 2007. DNA barcoding for the identification of smoked fish. Journal of Fish Biology 72:464-471
Stevanofa P, Taseva M, Georgieva T, Gotcheva V, Angelov A. 2013. A modified CTAB method for DNA extraction from soybean and meat products. Biotechnology & Biotechnological Equipment 27(3):3803-3810
Tamura K, Glen S, Daniel P, Alan F, Sudhir K. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 33(2):11-25
Udayasuriyan R, Bhavan PS, Vadivalagan C, Rajkumar G. 2015. Efficiency of different COI markers in DNA barcoding of freshwater prawn species. Journal of Entomology and Zoology Studies 3(3):98-110
Voloch CM, Freire PR, Russo CAM. 2005. Molecular phylogeny of penaeid shrimp inferred from two mitochondrial markers. Genetics and Molecular Research 4(4):668-678
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of The Royal Society B 360:1847-1857
Westermeier R. 2005. Electrophoresis in Preactice. Weinheim (GE): Wiley-VCH
Wulansari N, Nurilmala M, Nurjanah. 2015. Deteksi ikan tuna dan produk olahannya berbasis protein dan DNA barcoding. Jurnal Pengolahan Hasil Perikanan Indonesia. 18(2):119-127
Xiong X, Huang M, Yuang F, Lu L, Xiong X. 2019. Development and validation of a fast DNA extraction protocol for fish product. Food Analitical Methods 10: 1-11. DOI: 10.1007/s12161-019-01554-z.
Yakovchuk P, Ekaterina P, Maxim DF-K. 2006. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acid Research 34(2):564-574
Zein MSA, Sulandari S. 2009. Investigasi asal-usul ayam Indonesia menggunakan sekuen hypervariable-1 d-loop mtDNA. Veteriner Maret 10(1):41-49
Zella AP. 2013. Karakterisasi genom mitokondria ikan pada gen cytochrome oxydase subunit 1 (COI) dan cytochrome b (CytB). [Skripsi]. IPB University, Bogor. [Indonesian]
Zhang Q, Cheng Q, Guan W. 2009. Mitochondrial COI gene sequence variation and taxonomic status of three Macrobrachium species. Zoological Research 30(6):613-619
Zhou J, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology 62(2):316-322
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