Advances in DNA-based techniques for the detection of seafood species substitution on the commercial market

Journal of Laboratory Automation

Volumn 16, Issue 4, 2011, Pages 308-321

  Rasmussen Hellberg, Rosalee S ^a   Morrissey, Michael T ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

DNA based methods; Fish; PCR; Seafood; Species identification

Indexed keywords

COMMERCIAL MARKET; COMPLEMENTARY PROPERTY; DEOXYRIBONUCLEIC ACIDS; DNA ISOLATION; DNA MICRO-ARRAY; DNA-BASED METHODS; FRAGMENT LENGTHS; HIGH POTENTIAL; HIGH-THROUGHPUT; HIGH-THROUGHPUT OPERATION; IDENTIFICATION METHOD; LARGE-SCALE APPLICATIONS; MAGNETIC BEADS; MICROFLUIDIC CHIP; PCR; REAL-TIME PCR; SEAFOOD; SPECIES IDENTIFICATION; SPECIES SUBSTITUTION; TECHNOLOGICAL ADVANCES;

BIOASSAY; BIOCHIPS; COMMERCE; DNA; FISH; GENE ENCODING; MEATS; ORGANIC ACIDS; SILICA;

POLYMERASE CHAIN REACTION;

CYTOCHROME B; CYTOCHROME C OXIDASE SUBUNIT I; DNA; DNA FRAGMENT; FERROMAGNETIC MATERIAL; LOCKED NUCLEIC ACID; MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN; TAQ POLYMERASE; UNCLASSIFIED DRUG;

ANALYTIC METHOD; CHARACTER BASED ANALYSIS; DNA BARCODING; DNA DETERMINATION; DNA ISOLATION; DNA MICROARRAY; DNA MINIBARCODING; FOOD ANALYSIS; GENE TECHNOLOGY; HIGH THROUGHPUT SCREENING; LAB ON A CHIP; MAGNETIC BEAD TECHNOLOGY; MAGNETISM; MARKET; MULTIPLEX POLYMERASE CHAIN REACTION; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEIC ACID ANALYSIS; POLYMERASE CHAIN REACTION; PYROSEQUENCING; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SEA FOOD; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; SPECIES IDENTIFICATION;

ANIMALS; AUTOMATION, LABORATORY; BIVALVIA; DNA; DNA FINGERPRINTING; FISHES; HIGH-THROUGHPUT SCREENING ASSAYS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MOLECULAR TYPING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; SEAFOOD; SPECIES SPECIFICITY;

EID: 80053053912     PISSN: 22110682     EISSN: 22110690     Source Type: Journal    
DOI: 10.1016/j.jala.2010.07.004     Document Type: Review

References (140)

1. NOAA Fisheries: Office of Science and Technology Imports and exports of fishery products annual summary, 2009 Current Fisheries Statistics No. 2009-2,, (accessed May 17, 2010). http://www.st.nmfs.noaa.gov/st1/publications.html.
2. Voorhees D.V. Fisheries of the United States, 2008. National Marine Fisheries Service, Office of Science and Technology 2009, 39-55. Current Fisheries Statistics No. 2008, Silver Spring, Maryland, MD. E.S. Pritchard (Ed.).
3. U.S. Food and Drug Administration The Seafood List-FDA's guide to acceptable market names for seafood sold in interstate commerce (accessed May 17, 2010). http://www.fda.gov/Food/GuidanceComplianceRegulatoryInformation/GuidanceDocuments/Seafood/ucm113260.htm.
4. United States Government Accountability Office. Seafood Fraud: FDA program changes and better collaboration among key federal agencies could improve detection and prevention. GAO-09-258. A report to the Ranking Member, Subcommittee on Oceans, Atmosphere, Fisheries, and Coast Guard, Committee on Commerce Science, and Transportation, U.S. Senate; 2009.
5. Jacquet J.L., Pauly D. Trade secrets: renaming and mislabeling of seafood. Mar. Pol. 2008, 32:309-318.
6. Tennyson, J. M.; Winters, K. S.; Powell, K. A fish by any other name: a report on species substitution. In Papers presented at the 22nd annual meeting of Seafood Science the Technology Society of the Americas. Biloxi, MS, October 6-7, 1997, (accessed April 9, 2010). http://fshn.ifas.ufl.edu/seafood/sst/22ndAnn/file08.pdf.
7. Espiñeira M., Gonzalez-Lavin N., Vieites J.M., Santaclara F.J. Authentication of anglerfish species (Lophius spp) by means of polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) and forensically informative nucleotide sequencing (FINS) methodologies. J. Agric. Food Chem. 2008, 56(22):10594-10599.
8. Espiñeira M., Gonzalez-Lavin N., Vieites J.M., Santaclara F.J. Development of a method for the genetic identification of flatfish species on the basis of mitochondrial DNA sequences. J. Agric. Food Chem. 2008, 56:8954-8961.
9. Espiñeira M., Gonzalez-Lavin N., Vieites J.M., Santaclara F.J. Development of a method for the genetic identification of bivalve species based on mitochondrial 18S rRNA sequences. J. Agric. Food Chem. 2009, 57:495-502.
10. Espiñeira M., Gonzalez-Lavin N., Vieites J.M., Santaclara F.J. Development of a method for the identification of scombroid and common substitute species in seafood products by FINS. Food Chem. 2009, 117:698-704.
11. Espiñeira M., Vieites J.M., Santaclara F.J. Development of a genetic method for the identification of salmon, trout, and bream in seafood products by means of PCR-RFLP and FINS methodologies. Eur. Food Res. Technol. 2009, 229(5):785-793.
12. Wong E.H.K., Hanner R.H. DNA barcoding detects market substitution in North American seafood. Food Res. Int. 2008, 41:828-837.
13. Marko P.B., Lee S.C., Rice A.M., Gramling J.M., Fitzhenry T.M., McAlister J.S., Harper G.R., Moran A.L. Fisheries: mislabelling of a depleted reef fish. Nature 2004, 430(6997):309-310.
14. Rasmussen R.S., Morrissey M.T. DNA-based methods for the identification of commercial fish and seafood species. Compr. Rev. Food Sci. Food Saf. 2008, 7:280-295.
15. Carrera E., Garcia T., Cespedes A., Gonzalez I., Sanz B., Hernandez P., Martin R. Immunostick colorimetric ELISA assay for the identification of smoked salmon (Salmo salar), trout (Oncorhynchus mykiss) and bream (Brama raii). J. Sci. Food Agric. 1997, 74:547-550.
16. Asensio L., González I., Rodríguez M.A., Hernández P.E., García T., Martín R. Development of a monoclonal antibody for grouper (Epinephelus marginatus) and wreck fish (Polyprion americanus) authentication using an indirect ELISA. J. Food Sci. 2003, 68(6):1900-1903.
17. Teletchea F. Molecular identification methods of fish species: reassessment and possible applications. Rev. Fish Biol. Fisheries 2009, 19:265-293.
18. Chapela M.J., Sotelo C.G., Perez-Martin R.I., Pardo M.A., Perez-Villareal B., Gilardi P., Riese J. Comparison of DNA extraction methods from muscle of canned tuna for species identification. Food Control 2007, 18:1211-1215.
19. Pardo M.A., Perez-Villareal B. Identification of commercial canned tuna species by restriction site analysis of mitochondrial DNA products obtained by nested primer PCR. Food Chem. 2004, 86(1):143-150.
20. Hsieh H.S., Chai T.J., Hwang D.F. Using the PCR-RFLP method to identify the species of different processed products of billfish meats. Food Control 2007, 18:369-374.
21. Ivanova N.V., Dewaard J.R., Hebert P.D.N. An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol. Ecol. Notes 2006, 6(4):998-1002.
22. Richardson D.E., Vanwy J.D., Exum A.M., Cowen R.K., Crawford D.L. High-throughput species identification: from DNA isolation to bioinformatics. Mol. Ecol. Notes 2006, 7:199-207.
23. Hajibabaei M., deWaard J.R., Ivanova N.V., Ratnasingham S., Dooh R.T., Kirk S.L., Mackie P.M., Hebert P.D. Critical factors for assembling a high volume of DNA barcodes. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2005, 360(1462):1959-1967.
24. Steinke D., Zemlak T.S., Gavin H., Hebert P.D.N. DNA barcoding of Pacific Canada's fishes. Mar. Biol. 2009, 156(12):2641-2647.
25. Rasmussen R.S., Morrissey M.T., Hebert P.D.N. DNA barcoding of commercially important salmon and trout species (Oncorhynchus and Salmo) from North America. J. Agric. Food Chem. 2009, 57:8379-8385.
26. Yancy H.F., Zemlak T.S., Mason J.A., Washington J.D., Tenge B.J., Nguyen N.T., Barnett J.D., Savary W.E., Hill W.E., Moore M.M., Fry F.S., Randolph S.C., Rogers P.L., Hebert P.D.N. Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia. J. Food Prot. 2008, 71(1):456-458.
27. Berensmeier S. Magnetic particles for the separation and purification of nucleic acids. Appl. Microbiol. Biotechnol. 2006, 73:495-504.
28. Paleček E., Fojta M. Magnetic beads as versatile tools for electrochemical DNA and protein biosensing. Talanta 2007, 74(3):276-290.
29. Lin W.F., Hwang D.F. Application of PCR-RFLP analysis on species identification of canned tuna. Food Control 2007, 18:1050-1057.
30. Lin W.F., Hwang D.F. Application of species-specific PCR for the identification of dried bonito product (Katsuobushi). Food Chem. 2008, 106:390-396.
31. Lin W.F., Hwang D.F. A multiplex PCR assay for species identification of raw and cooked bonito. Food Control 2008, 19(9):879-885.
32. Chen Y.-J., Huang K.-M., Jen H.-C., Su M.-W., Liu S.-M., Hwang D.-F. Bighead carp meat adulterated in commercial milkfish ball products. J. Food Drug Anal. 2009, 17(3):178-182.
33. Chang C.M., Chiou L.F., Lin C.C., Shieh D.B., Lee G.B. Three-dimensional microfluidic chip for the extraction of mitochondrial DNA. Microfluid. Nanofluidics 2010, 9:489-498.
34. Bartlett S.E., Davidson W.S. FINS (forensically informative nucleotide sequencing): a procedure for identifying the animal origin of biological specimens. BioTechniques 1992, 12(3):408-411.
35. Hebert P.D.N., Cywinska A., Ball S.L., deWaard J.R. Biological identifications through DNA barcodes. Proc. Biol. Sci. 2003, 270:313-321.
36. Kimura M. A simple method of estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16:111-120.
37. Rasmussen R.S., Morrissey M.T. Application of DNA-based methods to identify fish and seafood substitution on the commercial market. Compr. Rev. Food Sci. Food Saf. 2009, 8:118-154.
38. Ward R.D., Hanner R., Hebert P.D.N. The campaign to DNA barcode all fishes, FISH-BOL. J. Fish Biol. 2009, 74:329-356.
39. Jerome M., Martinsohn J.T., Ortega D., Carreau P., Verrez-Bagnis V., Mouchel O. Toward fish and seafood traceability: anchovy species determination in fish products by molecular markers and support through a public domain database. J. Agric. Food Chem. 2008, 56(10):3460-3469.
40. Logan C.A., Alter S.E., Haupt A.J., Tomalty K., Palumbi S.R. An impediment to consumer choice: overfished species are sold as Pacific red snapper. Biol. Cons. 2008, 141:1591-1599.
41. Viñas J., Tudela S. A validated methodology for genetic identification of tuna species (genus Thunnus). PLoS One 2009, 4(10):e7606.
42. Hebert P.D.N., Ratnasingham S., deWaard J.R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond., B, Biol. Sci. 2003, 270:S96-S99.
43. deWaard J.R., Ivanova N.V., Hajibabaei M., Hebert P.D.N. Assembling DNA barcodes. Methods in Molecular Biology 2008, 275-294. Humana Press, Totawa, NJ. C. Cristofre Martin (Ed.).
44. Ardura A., Linde A.R., Moreira J.C., Garcia-Vazquez E. DNA barcoding for conservation and management of Amazonian commercial fish. Biol. Conserv. 2010, 143(6):1438-1443.
45. Holmes B.H., Steinke D., Ward R.D. Identification of shark and ray fins using DNA barcoding. Fisheries Res. 2009, 95:280-288.
46. Valdez-Moreno M., Ivanova N.V., Elías-Gutiérrez M., Contreras-Balderas S., Hebert P.D.N. Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. J. Fish Biol. 2009, 74(2):377-402.
47. Hubert N., Hanner R., Holm E., Mandrak N.E., Taylor E., Burridge M., Watkinson D., Dumont P., Curry A., Bentzen P., Zhang J., April J., Bernatchez L. Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 2008, 3(6):e2490.
48. Hajibabaei M., Smith M.A., Janzen D.H., Rodriguez J.J., Whitfield J.B., Hebert P.D.N. A minimalist barcode can identify a specimen whose DNA is degraded. Mol. Ecol. Notes 2006, 6:959-964.
49. Meusnier I., Singer G.A.C., Landry J.F., Hickey D.A., Hebert P.D.N., Hajibabaei M. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 2008, 9:214.
50. Hajibabaei, M. DNA barcoding 2.0: environmental monitoring using next-generation sequencing technologies. In Abstracts Volume of the Third International Barcode of Life Conference. Mexico City, Mexico, Nov 7-12, 2009.
51. Ivanova N.V., Borisenko A.V., Hebert P.D.N. Express barcodes: racing from specimen to identification. Mol. Ecol. Resour. 2009, 9(S1):35-41.
52. Applied Biosystems Application note: advances in fast PCR contribute to a fast resequencing workflow (accessed April 9, 2010). http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_053967.pdf.
53. Shokralla, S.; Meusnier, I.; Janzen, D. H.; Hallwachs, W.; Hebert, P.; Hajibabaei, M. Pyrosequencing for rapid mini-barcoding. In Abstracts Volume of the Third International Barcode of Life Conference. Mexico City, Mexico, Nov 7-12, 2009.
54. Dubey B., Meganathan P.R., Haque I. DNA mini-barcoding: an approach for forensic identification of some endangered Indian snake species. Forensic Sci. Int. Genet. 2011, 5(3):181-184.
55. Van Houdt J.K.J., Breman F.C., Virgilio M., De Meyer M. Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes. Mol. Ecol. Resour. 2010, 10(3):459-465.
56. Sarkar I.N., Planet P.J., DeSalle R. CAOS software for use in character-based DNA barcoding. Mol. Ecol. Resour. 2008, 8:1256-1259.
57. Wong E.H.K., Shivji M.S., Hanner R.H. Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Mol. Ecol. Resour. 2009, 9:243-256.
58. Lara A., Ponce de León J.L., Rodríguez R., Casane D., Côtes G., Bernatchez L., García-Machado E. DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts. Mol. Ecol. Resour. 2010, 10:421-430.
59. Lowenstein J.H., Amato G., Kolokotronis S.O. The real maccoyii: identifying tuna sushi with DNA barcodes-contrasting characteristic attributes and genetic distances. PLoS One 2009, 4(11):e7866.
60. Russell V.J., Hold G.L., Pryde S.E., Rehbein H., Quinteiro J., Rey-Mendez M., Sotelo C.G., Perez-Martin R.I., Santos A.T., Rosa C. Use of restriction fragment length polymorphism to distinguish between salmon species. J. Agric. Food Chem. 2000, 48(6):2184-2188.
61. Rea S., Storani G., Mascaro N., Stocchi R., Loschi A.R. Species identification in anchovy pastes from the market by PCR-RFLP technique. Food Control 2009, 20(5):515-520.
62. Hsieh C.-H., Chang W.-T., Chang H.C., Hsieh H.-S., Chung Y.-L., Hwang D.-F. Puffer fish-based commercial fraud identification in a segment of cytochrome b region by PCR-RFLP analysis. Food Chem. 2010, 121(4):1305-1311.
63. Rasmussen R.S., Morrissey M.T., Walsh J. Application of a PCR-RFLP method to identify salmon species in U.S. commercial products. J. Aquat. Food Prod. Technol. 2010, 19:3-15.
64. Nagase M., Maeta K., Aimi T., Suginaka K., Morinaga T. Authentication of flying-fish-meal content of processed food using PCR-RFLP. Fisheries Sci. 2009, 75(3):811-816.
65. Freire R., Fernandez-Tajez J., Mendez J. Identification of razor clams Ensis arcuatus and Ensis siliqua by PCR-RFLP analysis of ITS1 region. Fisheries Sci. 2008, 74:511-515.
66. Hold G.L., Russell V.J., Pryde S., Rehbein H., Quinteiro J., Rey-Mendez M., Sotelo C.G., Perez-Martin R.I., Santos A.T., Rosa C. Validation of a PCR-RFLP based method for the identification of salmon species in food products. Eur. Food Res. Technol. 2001, 212:385-389.
67. Hold G.L., Russell V.J., Pryde S.E., Rehbein H., Quinteiro J., Vidal R., Rey-Mendez M., Sotelo C.G., Perez-Martin R.I., Santos A.T., Rosa C. Development of a DNA-based method aimed at identifying the fish species present in food products. J. Agric. Food Chem. 2001, 49(3):1175-1179.
68. Sotelo C.G., Calo-Mata P., Chapela M.J., Perez-Martin R.I., Rehbein H., Hold G.L., Russell V.J., Pryde S., Quinteiro J., Izquierdo M., Rey-Mendez M., Rosa C., Santos A.T. Identification of flatfish (Pleuronectiforme) species using DNA-based techniques. J. Agric. Food Chem. 2001, 49(10):4562-4569.
69. Rehbein H., Sotelo C.G., Perez-Martin R.I., Chapela-Garrido M.J., Hold G.L., Russell V.J., Pryde S., Santos A.T., Rosa C., Quinteiro J., Rey-Mendez M. Differentiation of raw or processed eel by PCR-based techniques: restriction fragment length polymorphism analysis (RFLP) and single strand conformation polymorphism analysis (SSCP). Eur. Food Res. Technol. 2002, 214(2):171-177.
70. Calo-Mata P., Sotelo C.G., Perez-Martin R.I., Rehbein H., Hold G.L., Russell V.J., Pryde S., Quinteiro J., Rey-Mendez M., Rosa C., Santos A.T. Identification of gadoid fish species using DNA-based techniques. Eur. Food Res. Technol. 2003, 217:259-264.
71. Wolf C., Burgener M., Hubner P., Luthy J. PCR-RFLP analysis of mitochondrial DNA: differentiation of fish species. Lebensm. Wiss. Technol. 2000, 33(2):144-150.
72. Nebola M., Borilova G., Kasalova J. PCR-RFLP analysis of DNA for the differentiation of fish species in seafood samples. Bull. Vet. Inst. Pulawy 2010, 54:49-53.
73. Dooley J.J., Sage H.D., Clarke M.A., Brown H.M., Garrett S.D. Fish species identification using PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis: application to detect white fish species in food products and an interlaboratory study. J. Agric. Food Chem. 2005, 53(9):3348-3357.
74. Dooley J.J., Sage H.D., Brown H.M., Garrett S.D. Improved fish species identification by use of lab-on-a-chip technology. Food Control 2005, 16:601-607.
75. DeSalle R., Birstein V.J. PCR identification of black caviar. Nature 1996, 381:197-198.
76. Rocha-Olivares A. Multiplex haplotype-specific PCR: a new approach for species identification of the early life stages of rockfishes of the species-rich genus Sebastes Cuvier. J. Exp. Mar. Biol. Ecol. 1998, 231(2):279-290.
77. Shivji M., Clarke S., Pank M., Natanson L., Kohler N., Stanhope M. Genetic identification of pelagic shark body parts for conservation and trade monitoring. Conserv. Biol. 2002, 16(4):1036-1047.
78. Mendonça F.F., Hashimoto D.T., De-Franco B., Porto-Foresti F., Gadig O.B.F., Oliveira C., Foresti F. Genetic identification of lamniform and carcharhiniform sharks using multiplex-PCR. Conserv. Genet. Resour. 2010, 2(1):31-35.
79. Mendonça F.F., Hashimoto D.T., Porto-Foresti F., Oliveira C., Gadig O.B.F., De-Franco B., Foresti F. Identification of the shark species Rhizoprionodon lalandii and R. porosus (Elasmobranchii, Carcharhinidae) by multiplex PCR and PCR-RFLP techniques. Mol. Ecol. Resour. 2009, 9:771-773.
80. De-Franco B., Mendonça F.F., Hashimoto D.T., Porto-Foresti F., Oliveira C., Foresti F. Forensic identification of the guitarfish species Rhinobatos horkelli, R. percellens, and Zapteryx brevirostris using multiplex-PCR. Mol. Ecol. Resour. 2010, 10:197-199.
81. Rasmussen Hellberg R.S., Morrissey M.T., Hanner R.H. A multiplex PCR method for the identification of commercially important salmon and trout species (Oncorhynchus and Salmo) in North America. J. Food Sci. 2010, 75(7):C595-606.
82. Rocha-Olivares A., Chávez-González J.P. Molecular identification of dolphinfish species (genus Coryphaena) using multiplex haplotype-specific PCR of mitochondrial DNA. Ichthyol. Res. 2008, 55(4):389-393.
83. Pinhal D., Gadig O.B.F., Wasko A.P., Oliveira C., Ron E., Foresti F., Martins C. Discrimination of shark species by simple PCR of 5S rDNA repeats. Gen. Mol. Biol. 2008, 31(1 Suppl.):361-365.
84. Farrell E.D., Clarke M.W., Mariani S. A simple genetic identification method for Northeast Atlantic smoothhound sharks (Mustelus spp.). ICES J. Mar. Sci. 2009, 66:561-565.
85. Sebastian H., Haye P.A., Shivji M.S. Characterization of the pelagic shark-fin trade in north-central Chile by genetic identification and trader surveys. J. Fish Biol. 2008, 73:2293-2304.
86. Hubalkova Z., Kralik P., Kasalova J., Rencova E. Identification of gadoid species in fish meat by polymerase chain reaction (PCR) on genomic DNA. J. Agric. Food Chem. 2008, 56(10):3454-3459.
87. Mugue N.S., Barmintseva A.E., Rastorguev S.M., Mugue V.N., Barmintseva V.A. Polymorphism of the mitochondrial DNA control region in eight sturgeon species and development of a system for DNA-based species identification. Russ. J. Genet. 2008, 44(7):793-798.
88. Wang H., Guo X. Identification of Crassostrea ariakensis and related oysters by multiplex species-specific PCR. J. Shellfish Res. 2008, 27(3):481-487.
89. Durand J.D., Diatta M.A., Diop K., Trape S. Multiplex 16S rRNA haplotype-specific PCR, a rapid and convenient method for fish species identification: an application to West African Clupeiform larvae. Mol. Ecol. Resour. 2010, 10:568-572.
90. Catanese G., Manchado M., Fernandez-Trujillo A., Infante C. A multiplex-PCR assay for the authentication of mackerels of the genus Scomber in processed fish products. Food Chem. 2010, 122:319-326.
91. Fernández-Tajes J., Freire R., Méndez J. A simple one-step PCR method for the identification between European and American razor clams species. Food Chem. 2010, 118(4):995-998.
92. Apostolidis A.P., Georgiadis A., Karaiskou N., Sandaltzopoulos R. Reliable and rapid discrimination of congeneric species by mtDNA SNP analysis by multiplex PCR: application on three Trachurus and two Mullus fish species as model cases. Hydrobiologia 2008, 614:401-404.
93. Zhan A., Hu J., Hu X., Lu W., Wang M., Peng W., Hui M., Bao Z. Fast identification of scallop adductor muscles using species-specific microsatellite markers. Eur. Food Res. Technol. 2008, 227:353-359.
94. Asensio L., González I., Rojas M., García T., Martín R. PCR-based methodology for the authentication of grouper (Epinephelus marginatus) in commercial fish fillets. Food Control 2009, 20(7):618-622.
95. Asensio L., González I., Pavon M.A., García T., Martín R. An indirect ELISA and a PCR technique for the detection of grouper (Epinephelus marginatus) mislabeling. Food Addit. Contam. Part A Chem. Anal. Control Expo. Risk Assess. 2008, 25(6):677-683.
96. Asensio L. Application of multiplex PCR for the identification of grouper meals in the restaurant industry. Food Control 2008, 19(11):1096-1099.
97. Lam W.Y., Yeung A.C., Tang J.W., Ip M., Chan E.W., Hui M., Chan P.K. Rapid multiplex nested PCR for detection of respiratory viruses. J. Clin. Microbiol. 2007, 45(11):3631-3640.
98. Sung R.Y.T., Chan P.K.S., Tsen T., Li A.M., Lam W.Y., Yeung A.C.M., Nelson E.A.S. Identification of viral and atypical bacterial pathogens in children hospitalized with acute respiratory infections in Hong Kong by multiplex PCR assays. J. Med. Virol. 2009, 81:153-159.
99. Zhang C., Xing D. Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends. Nucleic Acids Res. 2007, 35(13):4223-4237.
100. Zhang Y., Ozdemir P. Microfluidic DNA amplification-a review. Anal. Chim. Acta 2009, 638(2):115-125.
101. Christensen T.B., Bang D.D., Wolff A. Multiplex polymerase chain reaction (PCR) on a SU-8 chip. Microelectron. Eng. 2008, 85(5-6):1278-1281.
102. Hird H.J., Hold G.L., Chisholm J., Reece P., Russell V.J., Brown J., Goodier R., MacArthur R. Development of a method for the quantification of haddock (Melanogrammus aeglefinus) in commercial products using real-time PCR. Eur. Food Res. Technol. 2005, 220:633-637.
103. Watanabe S., Minegishi Y., Yoshinaga T., Aoyama J., Tsukamoto K. A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys. Mar. Biotechnol. 2004, 6(6):566-574.
104. Bertoja G., Giaccone V., Carraro L., Mininni A.N., Cardazzo B. A rapid and high-throughput real-time PCR assay for species identification: application to stockfish sold in Italy. Eur. Food Res. Technol. 2009, 229:191-195.
105. Trotta M., Schonhuth S., Pepe T., Cortesi M.L., Puyet A., Bautista J.M. Multiplex PCR method for use in real-time PCR for identification of fish fillets from grouper (Epinephelus and Mycteroperca species) and common substitute species. J. Agric. Food Chem. 2005, 53(6):2039-2045.
106. Vadopalas B., Bouma J.V., Jackels C.R., Friedman C.S. Application of a real-time PCR for simultaneous identification and quantification of larval abalone. J. Exp. Mar. Biol. Ecol. 2006, 334:219-228.
107. Koskela K.A., Matero P., Blatny J.M., Fykse E.M., Olsen J.S., Nuotio L.O., Nikkari S. A multiplatform real-time polymerase chain reaction detection assay for Vibrio cholerae. Diagn. Microbiol. Infect. Dis. 2009, 65(3):339-344.
108. Wang J.-H., Chien L.-J., Hsieh T.-M., Luo C.-H., Chou W.-P., Chen P.-H., Chen P.-J., Lee D.-S., Lee G.-B. A miniaturized quantitative polymerase chain reaction system for DNA amplification and detection. Sens. Actuators B. Chem. 2009, 141(1):329-337.
109. Lopez I., Pardo M.A. Application of relative quantification TaqMan real-time polymerase chain reaction technology for the identification and quantification of Thunnus alalunga and Thunnus albacares. J. Agric. Food Chem. 2005, 53(11):4554-4560.
110. Kutyavin I.V., Afonina I.A., Mills A., Gorn V.V., Lukhtanov E.A., Belousov E.S., Singer M.J., Walburger D.K., Lokhov S.G., Gall A.A., Dempcy R., Reed M.W., Meyer R.B., Hedgpeth J. 3'-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res. 2000, 28(2):655-661.
111. Ugozzoli L.A., Latorra D., Pucket R., Arar K., Hamby K. Real-time genotyping with oligonucleotide probes containing locked nucleic acids. Anal. Biochem. 2004, 324:143-152.
112. Taylor M.I., Fox C., Rico I., Rico C. Species-specific TaqMan probes for simultaneous identification of (Gadus morhua L.), haddock (Melanogrammus aeglefinus L.) and whiting (Merlangius merlangus L.). Mol. Ecol. Notes 2002, 2:599-601.
113. Itoi S., Nakaya M., Kaneko G., Kondo H., Sezaki K., Watabe S. Rapid identification of eels Anguilla japonica and Anguilla anguilla by polymerase chain reaction with single nucleotide polymorphism-based specific probes. Fisheries Sci. 2005, 71:1356-1364.
114. Bayha K.M., Graham W.M., Hernandez F.J. Multiplex assay to identify eggs of three fish species from the northern Gulf of Mexico, using locked nucleic acid Taqman real-time PCR probes. Aquat. Biol. 2008, 4:65-73.
115. King R.A., Read D.S., Traugott M., Symondson W.O.C. Molecular analysis of predation: a review of best practice for DNA-based approaches. Mol. Ecol. 2008, 17:947-963.
116. Dufva M. Fabrication of high quality microarrays. Biomol. Eng. 2005, 22:173-184.
117. Kochzius M., Nölte M., Weber H., Silkenbeumer N., Hjörleifsdottir S., Hreggvidsson G.O., Marteinsson V., Kappel K., Planes S., Tinti F., Magoulas A., Garcia Vazquez E., Turan C., Hervet C., Campo Falgueras D., Antoniou A., Landi M., Blohm D. DNA microarrays for identifying fishes. Mar. Biotechnol. 2008, 10(2):207-217.
118. Kochzius M. Trends in fishery genetics. The Future of Fisheries Science in North America 2009, 453-493. Springer Science+Business Media B.V., Dordrecht, Netherlands. R.J. Beamish, B.J. Rothschild (Eds.).
119. ® system. Eur. Food Res. Technol. 2008, 228:39-45.
120. Teletchea F., Bernillon J., Duffraisse M., Laudet V., Hänni C. Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples. J. Appl. Ecol. 2008, 45:967-975.
121. Zahariev M., Dahl V., Chen W., Levesque C.A. Efficient algorithms for the discovery of DNA oligonucleotide barcodes from sequence databases. Mol. Ecol. Resour. 2009, 9(Suppl. 1):58-64.
122. Chen W., Seifert K.A., Levesque C.A. A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium. Mol. Ecol. Resour. 2009, 9(Suppl. 1):114-129.
123. Hadidi A., Czosnek H., Barba M. DNA microarrays and their potential applications for the detection of plant viruses, viroids, and phytoplasmas. J. Plant Pathol. 2004, 86(2):97-104.
124. Pemov A., Modi H., Chandler D.P., Bavykin S. DNA analysis with multiplex microarray-enhanced PCR. Nucleic Acids Res. 2005, 33(2):1-9.
125. Huber M., Mündlein A., Dornstauder E., Schneeberger C., Tempfer C.B., Mueller M.W., Schmidt W.M. Accessing single nucleotide polymorphisms in genomic DNA by direct multiplex polymerase chain reaction amplification on oligonucleotide microarrays. Anal. Biochem. 2002, 303:25-33.
126. Khodakov D.A., Zakharova N.V., Gryadunov D.A., Filatov F.P., Zasedatelev A.S., Mikhailovich V.M. An oligonucleotide microarray for multiplex real-time PCR identification of HIV-1, HBV, and HCV. BioTechniques 2008, 44:241-248.
127. Metzker M.L. Sequencing technologies-the next generation. Nat. Rev. Genet. 2010, 11:31-46.
128. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 1977, 74:5463-5467.
129. Mardis E.R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 2008, 9:387-402.
130. Shendure J., Ji H. Next-generation DNA sequencing. Nat. Biotechnol. 2008, 26(10):1135-1145.
131. Coombs A. The sequencing shakeup. Nat. Biotechnol. 2008, 26(10):1109-1112.
132. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001, 11:3-11.
133. Boyanton J.B.L., Luna R.A., Fasciano L.R., Menne K.G., Versalovic J. DNA pyrosequencing-based identification of pathogenic Candida species by using the internal transcribed spacer 2 region. Arch. Pathol. Lab. Med. 2008, 132(4):667-674.
134. Tuohy M.J., Hall G.S., Sholtis M., Procop G.W. Pyrosequencing as a tool for the identification of common isolates of Mycobacterium sp. Diagn. Microbiol. Infect. Dis. 2005, 51:245-250.
135. Luna R.A., Fasciano L.R., Jones S.C., Boyanton B.L., Ton T.T., Versalovic J. DNA pyrosequencing-based bacterial pathogen identification in a pediatric hospital setting. J. Clin. Microbiol. 2007, 45(9):2985-2992.
136. Karlsson A.O., Holmlund G. Identification of mammal species using species-specific DNA pyrosequencing. Forensic Sci. Int. 2007, 173:16-20.
137. Balitzki-Korte B., Anslinger K., Bartsch C., Rolf B. Species identification by means of pyrosequencing the mitochondrial 12S rRNA gene. Int. J. Legal Med. 2005, 119:291-294.
138. Binladen J., Gilbert M.T.P., Bollback J.P., Panitz F., Bendixen C., Nielsen R., Willerslev E. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2007, 2:e197.
139. Meyers M., Stenzel U., Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat. Protoc. 2008, 3(2):267-278.
140. Hudson M.E. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol. Ecol. Notes 2007, 8:3-17.