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METHODS OF MOLECULAR DIAGNOSTICS FOR FISH SPECIES IDENTIFICATION

https://doi.org/10.21323/2618-9771-2020-3-3-32-41

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Abstract

The growth in demand for fish products as a result of globalization of trade caused a risks and threats of selling poor-quality and falsified fish products. This has become a great problem both for supervising agencies and for consumers.

Many countries have regulations on food labelling and safety. For example, in the Russian Federation, Republic of Belarus and Republic of Kazakhstan has been passed the Technical Regulation of the Customs Union TR CU022/2011 “Food products in part of their labeling” that aims to prevent misinformation of consumers to ensuring realization of consumer rights to reliable information about food products, and Technical Regulation TR EAEU040/2016 “On safety of fish and fish products” requires indication of the zoological name of the species of the aquatic biological resource or the object of aquaculture.

Fish species identification is traditionally carried out based on external morphological traits. However, it becomes impossible to identify species by ichthyological traits upon fish cutting, if the head and fins are removed, and the body is cut on pieces (especially, in case of fillets) and even more so upon technological processing. In this case, objective analytical methods of species identification are used, which are based on ELISA or PCR. However, DNA‑based methods have several advantages compared to ELISA methods and complement traditional morphological identification methods. This paper gives a wide overview of the most recent and used methods of fish species identification based on DNA analysis such as single-strand conformation polymorphism (SSCP) analysis, species-specific PCR, real-time PCR, polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP), DNA barcoding, Sanger sequencing and next-generation sequencing (NGS).

About the Authors

T. A. Fomina
V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences; National Centre for Safety of Aquatic Fisheries Products and Aquaculture
Russian Federation

Tatyana A. Fomina — candidate of technical sciences, senior research scientist, Laboratory of Molecular Biology and Bioinformatics

109316, Moscow, Talalikhina str., 26

Head of the Department of molecular diagnostic research at the testing reference laboratory

129626, Moscow, Grafskiy per., 14–1. Tel.: +7–903–732–74–19



V. Yu. Kornienko
V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences
Russian Federation

Vladimir Yu. Kornienko — candidate of biological sciences, senior research scientist, Laboratory of Molecular Biology and Bioinformatics

109316, Moscow, Talalikhina str., 26. Tel.: +7–495–676–60–11



M. Yu. Minaev
V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences
Russian Federation

Mikhail Yu. Minaev — candidate of technical sciences, head of Laboratory of Molecular Biology and Bioinformatics

109316, Moscow, Talalikhina str., 26. Tel.: +7–495–676–60–11



References

1. Ferrito, V., A. Pappalardo, A.M. (2017). Seafood species identification by DNA barcoding, a molecular tool for food traceability. Biodiversity Journal, 8(1), 65–72.

2. Carrera, M., Cañas, B., Gallardo, J.M. (2013). Fish Authentication. Chapter in the book Proteomics in Foods, 205–222. https://doi.org/10.1007/978–1–4614–5626–1_12, ISBN 978–1–4614–5625–4

3. Jacquet, J.L., Pauly, D. (2008). Trade Secrets: Renaming and Mislabeling of Seafood. Marine Policy, 32(3), 309–318. https://doi.org/10.1016/j.marpol.2007.06.007

4. von den Heyden, S., Barendse, J., Seebregts, A.J., Mattee, C.A. (2010). Misleading the masses: Detection of Mislabelled and Substituted Frozen Fish Products in South Africa. ICES Journal of Marine Science, 67(1), 176–185. https://doi.org/10.1093/icesjms/fsp222

5. Miller, D.D., Mariani, S. (2010). Smoke, mirrors and mislabeled cod: Poor transparency in the European seafood industry. Frontiers in Ecology and the Environment, 8(10), 517–521. https://doi.org/10.1890/090212

6. Chandrika, M, Maimunah, M, Zainon, M.N., Son, R. (2010). Identification of the species origin of commercially available processed food products by mitochondrial DNA analysis. International Food Research Journal, 17(4), 867–876.

7. Patel, R.R., Thakkar, N.J., Shah, P.D., Mankodi, P.C. (2018). Species confirmation and evaluation of nutritive values of frozen fish products. International Journal of Food Science and Nutrition, 3(2), 58–63.

8. Regulation (EU) No 1169/2011 of 25 October 2011 on the provision of food information to consumers, amending Regulations (EC) No. 1924/2006 and (EC) No. 1925/2006 of the European Parliament and of the Council, and repealing Commission Directive 87/250/EEC, Council Directive 90/496/EEC, Commission Directive 1999/10/EC, Directive 2000/13/EC of the European Parliament and of the Council, Commission Directives 2002/67/EC and 2008/5/EC and Commission Regulation (EC) No 608/2004. Official Journal of the European Union, L304, 18–63.

9. Technical regulations of the Customs Union TR CU022/2011 “Food products in terms of its labeling” (approved by the decision of the customs Union Commission of December 9, 2011 № 880) (as amended on September 14, 2018). Moscow. — 2011. (in Russian)

10. Esakova, N. V. Pampura, A.N., Varlamov, E.E., Okuneva, T.S. (2017). Clinical and immunological features of anaphylaxis to fish in children. Experimental and clinical gastroenterology journal, 1(137), 78–82. (In Russian)

11. Sharp, M. F., Lopata, A. L. (2014). Fish allergy: In review. Clinical Reviews in Allergy and Immunology, 46(3), 258–271. https://doi.org/10.1007/s12016–013–8363–1

12. Pampura, A.N., Varlamov E. E. (2019). The clinical significance of food animal allergens. Russian Journal of Allergy, 16(1–1), 29–35. (In Russian)

13. Telmo J. R. Fernandes, Joana Costa, M. Beatriz P. P. Oliveira, Isabel Mafra. Telmo J. R. Fernandes, T.J.R., Costa, J., Oliveira, M.B. P.P., Mafra, I. (2018). Exploiting 16S rRNA gene for the detection and quantification of fish as a potential allergenic food: A comparison of two real-time PCR approaches. Food Chemistry, 45, 1034–1041. https://doi.org/10.1016/j.foodchem.2017.11.068

14. Namazatova-Baranova, L.S. (2011). Allergy in children: from theory to practice. Moscow: The Union of pediatricians of Russia. — 668 p. ISBN 978–5–904753–06–1 (In Russian)

15. Kuprina, E.E. (2015). Identification of commercial hydrobionts by ichthyological and instrumental methods. St. Petersburg: ITMO University. — 110 p. (In Russian)

16. Teletchea, F. (2009). Molecular identification methods of fish species: reassessment and possible applications. Reviews in Fish Biology and Fisheries, 19(3), 265–293. https://doi.org/10.1007/s11160–009–9107–4

17. Boidya, P., Haque, W., Rahman, M.M. (2015). Molecular identification and phylogenetic assessment of some marine catfishes of the bay of bengal. International Journal of Pure and Applied Zoology, 3(4), 279–286.

18. Pozdnyakovskiy, V.M., Ryazanova, O.A., Kalenik, T.K., Datsun, V.M. (2007). Inspection of fish, fish products and non-fish objects of aquatic harvesting. Quality and safety. Novosibirsk: Siberian University Publishing House. — 306 p. ISBN 5–94087–041–4 (In Russian)

19. Minchenko, A.G., Dudareva, N.A. (1990). The mitochondrial genome. Novosibirsk: Nauka. — 194 p. ISBN 5–02–029553–1 (In Russian)

20. Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature, 362(6422), 709–715. https://doi.org/10.1038/362709a0

21. Modica-Napolitano, J.S., Singh, K. (2002). Mitochondria as targets for detection and treatment of cancer. Expert Reviews in Molecular Medicine, 4(9), 1–19. https://doi.org/10.1017/s1462399402004453

22. Petros, J.A., Baumann, A.K., Ruiz-Pesini, E., Amin, M.B., Sun, C.Q., Hall, J., Lim, S.-D., Issa, M.M., Flanders, W.D., Hosseini, S.H., Marshall, F.F., Wallace, D.C. (2005). mtDNA mutations increase tumorigenicity in prostate cancer. Proceedings of the National Academy of Sciences of the United States of America, 102(3), 719–724. https://doi.org/10.1073/pnas.0408894102

23. Richter, C. (1987). Biophysical consequence of lipid peroxidation in membranes. Chemistry and Physics of Lipids, 44(2–4), 175–189. https://doi.org10.1016/0009–3084(87)90049–1

24. Nurgalieva, A. Kh., Karunas, A.S., Khusainova, R.I., Khidiyatova, I.M., Akhmetova, V.L., Valiev, R.R., Nadyrshina, D.D., Mustafin, R.N., Murzabaeva, S. Sh., Khusnutdinovs, E.K. (2013). Molecular-genetic methods for studying human hereditary diseases. Ufa: Bashkir State University. — 102 p. (In Russian)

25. Sunnucks, P., Wilson, A.C.C., Beheregaray, L.B., Zenger, French, K.J., Taylor, A.C. (2000). SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Molecular Ecology, 9(11), 1699–1710. https://doi.org/10.1046/j.1365–294x.2000.01084.x

26. Konstantinos, K. V., Panagiotis, P., Antonios, V. T., Agelos, P., Argiris, N.V. (2008). PCR–SSCP: A Method for the Molecular Analysis of Genetic Diseases. Molecular Biotechnology, 38(2), 155–163. https://doi.org/10.1007/s12033–007–9006–7

27. Weder, J., Rehbein, H., Kaiszer, K.-P. (2001). On the specificity of tuna-directed primes in PCR-SSCP analysis of fish and meat. European Food Research and Technology, 213(2),139–144. https://doi.org/10.1007/s002170100339

28. Ludwig, A. Identification of Acipenseriformes species in Trade. [Electronic resource: http://awsassets.panda.org/downloads/24_2008_identification_acipenseriformes_in_trade_iucn_int.pdf Access date 25.05.2020]

29. Spychaj, A., Mozdziak, P.E., Pospiech, E. (2009). PCR methods in meat species identification as a tool for the verification of regional and traditional meat products. Acta Scientiarum Polonorum Technologia Alimentaria, 8(2), 5–20.

30. Bobo, L.D. (1993). PCR Detection of Chlamydia trachomatis. Diagnostic. Molecular Microbiology. Principles and Applications. Washington: ASM Press. — P. 235–241.

31. Birstein, V.J., Doukakis, P., Sorkin, B., DeSalle, R. (1998). Population aggregation analysis of three caviar-producing species of sturgeons and implications for the species identification of black caviar. Conservation Biology, 12(4), 766–775. https://doi.org/10.1046/j.1523–1739.1998.97081.x

32. Doukakis, P., Birstein, V. J., Ruban, G. I., DeSalle, R. (1999). Molecular genetic analysis among subspecies of two Eurasian sturgeon species, Acipenser baerii and A. stellatus. Molecular Ecology, 8(s1), S117-S127. https://doi.org/10.1046/j.1365–294X.1999.00816.x

33. Coşier, V. (2019). Multiplex PCR assay for detection and identification of animal species in the meat products. Lucrari Stiintifice. Seria Zootehnie, 72, 215–220.

34. Michelini, E., Cevenini, L., Mezzanotte, L., Simoni, P., Baraldini, M., De Laude, L., Roda, A. (2007). One-step triplex-polymerase chain reaction assay fot the authentication of yellowfin (Thunnus albacares), bigeye (Thunnus obesus), and skipjack (Katsuwonus pelamis) tuna DNA from fresh, frozen, and canned tuna samples. Journal of Agricultural and Food Chemistry, 55(19), 7638–7647. https://doi.org/10.1021/jf070902k

35. Higuchi, R., Fockler, C., Dollinger, G., Watson, R. (1993). Kinetic PCR Analysis: Real-time monitoring of DNA amplification reaction. Nature Biotechnology, 11(9), 1026–1030. https://doi.org/10.1038/nbt0993–1026

36. Heid, C.A., Stevens, J., Livak, K.J., Williams, P.M. (1996). Real-time quantitative PCR. Genome Research, 6(10), 986–994. https://doi.org/10.1101/gr.6.10.986

37. Ekimov, A.N., Shipulin, G.A., Bochkarev, E.G., Rumin, D. V. Real-Time PCR. [Electronic resource: https://www.interlabservice.ru/catalog/faq/?id=3422 Access date 11.05.2020] (In Russian)

38. Tyagi, S., Kramer, F.R. (1996). Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnology, 14(3), 303–308. https://doi.org/10.1038/nbt0396–303

39. Hird, H. J., Hold, G. L., Chisholm, J., Reece, P., Russell, V.J., Brown, J., Goodier, R., MacArthur, R. (2005). Development of a method for the quantification of haddock (Melanogrammus aeglefinus) in commercial products using real-time PCR. European Food Research and Technology, 220(5–6), 663–637. https://doi.org/10.1007/s00217–004–1050-y

40. Sánchez, A., Quinteiro, J., Vázquez, J.A., Perez-Martín, R.I., Sotelo, C.G. A. (2019). Comparison of real-time PCR methods for quantification of European hake (Merluccius merluccius) in processed food samples. Food Chemistry, 272, 279–285. https://doi.org/10.1016/j.foodchem.2018.08.031

41. Tyulkin, S.V., Vafin, R.R., Muratova, A.V., Khatypov, I.I., Zagidullin, L.R., Rachkova, E.N., Akhmetov, T.M., Ravilov, R.K. (2015). Development of a method for PCR-RFLP on the example of dgat1 gene in cattle. Fundamental research, 2–17, 3773–3775. (in Russian)

42. Hebert, P.D.N., Cywinska, A., Ball, S.L., deWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), 313–321. https://doi.org/10.1098/rspb.2002.2218

43. Gil, L.A. (2007). PCR — based methods for fish and fishery products authentication. Trends in Food Science and Technology, 18(11), 558–566. https://doi.org/10.1016/j.tifs.2007.04.016

44. Hold, G.L., Russell, V.J., Pryde, S.E., Rehbein, H., Quinteiro, J., Rey-Mendez, M., Sotelo, C.G., Pérez-Martin, R.I., Santos, A.T., Rosa, C. (2001). Validation of a PCR-RFLP based method for the identification of salmon species in food products. European Food Research and Technology, 212(3), 385–389. https://doi.org/10.1007/s002170000237

45. Russell, V.J., Hold, G.L., Pryde, S.E., Rehbein, H., Quinterio, J., Rey-Mendez, M., Sotelo, C.G., Pérez-Martin, R.I., Santos, A., Rosa, C. (2000). Use of restriction fragment length polymorphism (RFLP) to distinguish between salmon species. Journal of Agricultural and Food Chemistry, 48(6), 2184–2188. https://doi.org/10.1021/jf991213e

46. Lin, W.-F., Hwang, D.-F. (2007). Application of PCR-RFLP analysis on species identification of canned tuna. Food Control, 18(9), 1050–1057. https://doi.org/10.1016/j.foodcont.2006.07.001

47. Wu, Ya-J., Hsieh, C.-H., Chen, H.-M., Hwang, D.-F. (2008). Identification of six common species of processed filefish using, cytochrome b gene sequence and PCR-RFLP analysis. The raffles bulletin of zoology, 19, 151–158.

48. Mueller, S., Ravi, H., Novoradovskaya, N., Kincaid, R., Chee, Y.-L. (2011). Enhanced fish species identification by PCR-RFLP using the 2100 Bioanalyzer system. International Food Research Journal, 18(3), 1209–1213.

49. Dooley, J. J., Sage, H. D., Brown, H. M., Garrett, S. D. (2004). Improved fish species identification by use of lab-on-a-chip technology. Food Control, 16(7), 601–607. https://doi.org/10.1016/j.foodcont.2004.06.022

50. Formosa, R., Ravi, H., Happe, S., Huffman, D., Novoradovskaya, N., Kincaid, R., Garrett, S. (2010). DNA‑based Fish Species Identification Protocol. Journal of Visualized Experiments, 38, e1871. https://doi.org/10.3791/1871

51. Zakharov, I.A., Shaikevich, E.V., Ivshin, N.V. (2007). DNA‑barcoding in entomology. Priroda, 9(1105), 3–9. (In Russian)

52. What is DNA Barcoding? [Electronic resource: www.ibol.org. Access date 12.06.2020]

53. Shekhovtsov, S.V., Shekhovtsova, I.N., Peltek S. E. (2019). DNA barcoding: methods and approaches. Uspehi sovremennoj biologii, 139(3), 211–220. https://doi.org/10.1134/S0042132419030074 (In Russian)

54. Ward, R.D., Hanner, R., Hebert, P.D.N. (2009). The Campaign to DNA Barcode All Fishes, FISH-BOL. Journal of Fish Biology, 74(2), 329–356. https://doi.org/10.1111/j.1095–8649.2008.02080.x

55. Janzen, D.H. (2004) Now is the time. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 359(1444), 731–732. https://doi.org/10.1098/rstb.2003.1444

56. Lipscomb, D., Platnick, N., Wheeler, Q. (2003). The intellectual content of taxonomy: a comment on DNA taxonomy. Trends in Ecology and Evolution, 18(2), 65–66. https://doi.org/10.1016/s0169–5347(02)00060–5

57. Soininen E. M., Valentini A., Coissac E., Miquel C., Gielly L., Brochmann C., Brysting A. K., Sønstebø J. H., Ims R. A., Yoccoz N. G., Taberlet P. (2009). Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in zoology, 6(1), 16. https://doi.org/10.1186/1742–9994–6–16

58. Mallet, J, Willmott, K (2003). Taxonomy: renaissance or Tower of Babel? Trends in Ecology and Evolution, 18, 57–59. https://doi.org/10.1016/s0169–5347(02)00061–7

59. Moritz, C, Cicero, C. (2004). DNA barcoding: promise and pitfalls. PLoS Biology, 2(10), e354. https://doi.org/10.1371/journal.pbio.0020354

60. Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A., Janzen, D. H. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America, 102(23), 8369–8374. https://doi.org/10.1073/pnas.0503123102

61. Barcaccia, G., Lucchin, M., Cassandro, M. (2015). DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy. Diversity. 8(4), 2. https://doi.org/10.3390/d8010002.

62. Fiers, W., Contreras, R., Haegeman, G., Rogiers, R., Van de Voorde, A., Heuverswyn, H. V., Herreweghe, J.V., Volckaert, G., Ysebaert, M. (1978). Complete nucleotide sequence of SV40 DNA. Nature, 273(5658), 113–120. https://doi.org/10.1038/273113a0

63. Reddy, V.B., Thimmappaya, B., Dhar, R., Subramania, K.N., Zain, B.S., Pan, J., Ghosh, P.K., Celma, M.L., Weissman, S.M. (1978). The genome of simian virus 40. Science, 200(4341), 494–502. https://doi.org/10.1126/science.205947

64. Sanger, F., Coulson, A.R. (1975). A rapid method for determining sequences in DNA by primed syntesis with DNA polymerase. Journal of Molecular Biology, 94(3), 444–448. https://doi.org/10.1016/0022–2836(75)90213–2

65. Budilov, A. Methods for deciphering nucleotide sequences of DNA fragments. [Electronic resource: http://molbiol.ru/protocol/13_03.html Access date 20.05.2020] (In Russian)

66. Nedoluzhko A. (2017). Methods in pictures: sequencing of nucleic acids. [Electronic resource: https://www.researchgate.net/publication/319058696 Access date 01.06.2020] (in Russian)

67. GOST 34106–2017. “Food and raw materials. Sequencing of the mitochondrial genomes of animals and fish for species identification in single component products”. Moscow: Standartinform. 2017. —21 p. (In Russian)

68. MR № 4.0002–15 “Fish and fish products. Methods for species identification based on sequencing of amplified DNA fragments”. Moscow: VNIIMP. —20 p. (In Russian)

69. Standard Nucleotide BLAST [Electronic resource: http://blast.ncbi.nlm.nih.gov/Blast.cgi? PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome Access date 10.06.2020]

70. Zubov, V. Next Generation Sequencing Technologies (Draft Roadmap). [Electronic resource: http://bioinformatics.ru/Misc/genseq-roadmap.html Access date 01.06.2020] (In Russian)


For citation:


Fomina T.A., Kornienko V.Yu., Minaev M.Yu. METHODS OF MOLECULAR DIAGNOSTICS FOR FISH SPECIES IDENTIFICATION. Food systems. 2020;3(3):32-41. https://doi.org/10.21323/2618-9771-2020-3-3-32-41

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