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Species and lineage identification for yellowfin Thunnus albacares and bigeye T. obesus tunas using two independent multiplex PCR assays

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Abstract

Based on nucleotide substitutions in four mitochondrial DNA regions, we developed multiplex PCR assays for identifying species/lineages in yellowfin Thunnus albacares and bigeye T. obesus tunas. The validity of the assays was tested on 3247 individuals of seven Thunnus tuna species (T. orientalis, T. thynnus, T. maccoyii, T. alalunga, T. albacares, T. obesus, and T. tonggol). Bigeye and yellowfin tunas were almost completely discriminated. Of the two intraspecific mitochondrial lineages—alpha (clade II) and beta (clade I)—of bigeye tuna, the former is known to predominate in the Atlantic but to be almost nonexistent in the Indo-Pacific. The multiplex PCR methods we developed were able to discriminate these two lineages. These multiplex PCR assays were more rapid and robust than conventional methods for identifying these tunas and their intraspecific lineages.

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References

  1. Fonteneau A, Ariz J, Delgado A, Pallares P, Pianet R (2005) A comparison of bigeye Thunnus obesus stocks and fisheries in the Atlantic, Indian and Pacific Oceans. Col Vol Sci Pap ICCAT 57:41–66

    Google Scholar 

  2. Satou K, Okamoto H, Fukuda T, Nohara K, Sasaki Y, Ooshima T (2010) Accuracy of species identification of yellowfin and bigeye in three canneries of Kingdom of Thailand (SC6-2010/ST-WP-04). WCPFC, Kolonia

  3. Chow S, Inoue S (1993) Intra-and interspecific restriction fragment length polymorphism in mitochondrial genes of Thunnus tuna species. Bull Natl Res Inst Far Seas Fish 30:619–627

    Google Scholar 

  4. Chow S, Kishino H (1995) Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): inconsistent implications from morphology, nuclear and mitochondrial genomes. J Mol Evol 41:741–748

    Article  CAS  PubMed  Google Scholar 

  5. Mackie IM, Pryde SE, Gonzales-Sotelo C, Medina I, Perez-Martin R, Quinteiro J, Rey-Mendez M, Rehbein H (1999) Challenges in the identification of species of canned fish. Trends Food Sci Technol 10:9–14

    Article  CAS  Google Scholar 

  6. Chow S, Okamoto H, Miyabe N, Hiramatsu K (2000) Genetic divergence between Atlantic and Indo-Pacific stocks of bigeye tuna Thunnus obesus and admixture around South Africa. Mol Ecol 9:221–227

    Article  CAS  PubMed  Google Scholar 

  7. Smith PJ, Griggs L, Chow S (2001) DNA identification of Pacific bluefin tuna Thunnus orientalis in the NZ fishery. N Z J Mar Freshw 35:843–850

    Article  CAS  Google Scholar 

  8. Chow S, Nohara K, Tanabe T, Itoh T, Tsuji S, Nishikawa Y, Ueyanagi S, Uchikawa K (2003) Genetic and morphological identification of larval and small juvenile tunas (Pisces: Scombridae) caught by a mid-water trawl in the western Pacific. Bull Fish Res Agency 8:1–14

    Google Scholar 

  9. Lin WF, Shiau CY, Hwang DF (2005) Identification of four Thunnus tuna species using mitochondrial cytochrome b gene sequence and PCR-RFLP analysis. J Food Drug Anal 13:382–387

    CAS  Google Scholar 

  10. Lin WF, Hwang DF (2007) Application of PCR-RFLP analysis on species identification of canned tuna. Food Control 18:1050–1057

    Article  CAS  Google Scholar 

  11. Michelini E, Cevenini L, Mezzanotte L, Simoni P, Baraldini M, De Laude L, Roda A (2007) One-step triplex-polymerase chain reaction assay for the authentication of yellowfin Thunnus albacares, bigeye Thunnus obesus, and skipjack Katsuwonus pelamis tuna DNA from fresh, frozen, and canned tuna samples. J Agric Food Chem 55:7638–7647

    Article  CAS  PubMed  Google Scholar 

  12. Lockley AK, Bardsley RG (2000) A novel method for the discrimination of tuna (Thunnus thynnus) and bonito (Sarda sarda) DNA. J Agric Food Chem 48:4463–4468

    Article  CAS  PubMed  Google Scholar 

  13. Bottero MT, Dalmasso A, Cappelletti M, Secchi C, Civera T (2007) Differentiation of five tuna species by a multiplex primer-extension assay. J Biotechnol 129:575–580

    Article  CAS  PubMed  Google Scholar 

  14. Bartlett SE, Davidson WS (1992) FINS (forensically informative nucleotide sequencing): a procedure for identifying the animal origin of biological specimens. Biotechniques 12:408–411

    CAS  PubMed  Google Scholar 

  15. Alvarado-Bremer JR, Naseri I, Ely B (1997) Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region. J Fish Biol 50:540–554

    Google Scholar 

  16. Terol J, Mascarell R, Fernandez-Pedrosa V, Perez-Alonso M (2002) Statistical validation of the identification of tuna species: bootstrap analysis of mitochondrial DNA sequences. J Agric Food Chem 50:963–969

    Article  CAS  PubMed  Google Scholar 

  17. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc B 360:1847–1857

    Article  CAS  Google Scholar 

  18. Paine MA, McDowell JR, Graves JE (2007) Specific identification of western Atlantic Ocean scombrids using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene region sequences. Bull Mar Sci 80:353–367

    Google Scholar 

  19. Viñas J, Tudela S (2009) A validated methodology for genetic identification of tuna species (genus Thunnus). PLoS One 4:e7606

    Article  PubMed  PubMed Central  Google Scholar 

  20. Lowenstein JH, Amato G, Kolokotronis SO (2009) The real maccoyii: identifying tuna sushi with DNA barcodes—contrasting characteristic attributes and genetic distances. PLoS One 4:e7866

  21. Botti S, Giuffra E (2010) Oligonucleotide indexing of DNA barcodes: identification of tuna and other scombrid species in food products. BMC Biotechnol 10:60

    Article  PubMed  PubMed Central  Google Scholar 

  22. Tseng MC, Shiao JC, Hung YH (2011) Genetic identification of Thunnus orientalis, T. thynnus, and T. maccoyii by a cytochrome b analysis. Environ Biol Fishes 91:103–115

    Article  Google Scholar 

  23. Mitchell JK, Hellberg RS (2016) Use of the mitochondrial control region as a potential DNA mini-barcoding target for the identification of canned tuna species. Food Anal Methods 9:2711–2720. doi:10.1007/s12161-016-0460-3

  24. Lopez I, Pardo MA (2005) 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 53:4554–4560

  25. Dalmasso A, Fontanella E, Piatti P, Civera T, Secchi C, Bottero MT (2007) Identification of four tuna species by means of real-time PCR and melting curve analysis. Vet Res Commun 31:355–357

    Article  PubMed  Google Scholar 

  26. Terio V, Pinto PD, Decaro N, Parisi A, Desario C, Martella V, Buonavoglia C, Tantillo MG (2010) Identification of tuna species in commercial cans by minor groove binder probe real-time polymerase chain reaction analysis of mitochondrial DNA sequences. Mol Cell Probes 24:352–356

    Article  CAS  PubMed  Google Scholar 

  27. Chuang PS, Chen MI, Shiao JC (2012) Identification of tuna species by a real-time polymerase chain reaction technique. Food Chem 133:1055–1061

    Article  CAS  Google Scholar 

  28. Rehbein H, Mackie IM, Pryde S, Gonzales-Sotelo C, Pérez-Martín R, Quinteiro J, Rey-Méndez M (1995) Fish species identification in canned tuna by DNA analysis (PCR-SSCP). Inf Fischwirtsch 42:209–212

    Google Scholar 

  29. Rehbein H, Mackie IM, Pryde S, Gonzales-Sotelo C, Pérez-Martín R, Quinteiro J, Rey-Méndez M (1998) Comparison of different methods to produce single-strand DNA for identification of canned tuna by single-strand conformation polymorphism analysis. Electrophoresis 19:1381–1384

    Article  CAS  PubMed  Google Scholar 

  30. Rehbein H, Mackie IM, Pryde S, Gonzales-Sotelo C, Medina I, Pérez-Martín R, Quinteiro J, Rey-Méndez M (1999) Fish species identification in canned tuna by PCR-SSCP: validation by a collaborative study and investigation of intra-species variability of the DNA-patterns. Food Chem 64:263–268

    Article  CAS  Google Scholar 

  31. Colombo F, Mangiagalli G, Renon P (2005) Identification of tuna species by computer-assisted and cluster analysis of PCR–SSCP electrophoretic patterns. Food Control 16:51–53

    Article  CAS  Google Scholar 

  32. Kitaoka M, Okamura N, Ichinose H, Goto M (2008) Detection of SNPs in fish DNA: application of the fluorogenic ribonuclease protection (FRIP) assay for the authentication of food contents. J Agric Food Chem 56:6246–6251

    Article  CAS  PubMed  Google Scholar 

  33. Takeyama H, Tsuzuki H, Chow S, Nakayama H, Matsunaga T (2000) Discrimination between Atlantic and Pacific subspecies of northern bluefin tuna Thunnus thynnus by magnetic-capture hybridization using bacterial magnetic particles. Mar Biotechnol 2:309–313

    CAS  PubMed  Google Scholar 

  34. Tanaka T, Sasaki T, Amemiya Y, Takeyama H, Chow S, Matsunaga T (2006) Discrimination of DNA mismatches by direct force measurement for identification of tuna species. Anal Chim Acta 561:150–155

    Article  CAS  Google Scholar 

  35. Edwards MC, Gibbs RA (1994) Multiplex PCR: advantages, development, and applications. PCR Methods Appl 3:S65–S75

    Article  CAS  PubMed  Google Scholar 

  36. Alvarado-Bremer JR, Stequert B, Robertson NW, Ely B (1998) Genetic evidence for inter-oceanic subdivision of bigeye tuna Thunnus obesus populations. Mar Biol 132:547–557

    Article  Google Scholar 

Download references

Acknowledgments

We thank M. Michibayashi, H. Hasegawa, and K. Saito of the National Research Institute of Far Seas Fisheries, Japan, for their huge amount of technical assistance. This study was financially supported by the Japan Fisheries Agency.

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Authors and Affiliations

  1. National Research Institute of Far Seas Fisheries, 5-7-1, Orido, Shimizu, Shizuoka, 424-8633, Japan

    Ryouichi Higashi, Kay Sakuma, Satoru N. Chiba, Nobuaki Suzuki, Yasuko Semba & Hiroaki Okamoto

  2. National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan

    Seinen Chow

  3. School of Marine Science and Technology, Tokai University, 3-20-1, Orido, Shimizu, Shizuoka, 424-8610, Japan

    Kenji Nohara

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  1. Ryouichi Higashi
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  2. Kay Sakuma
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  3. Satoru N. Chiba
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  4. Nobuaki Suzuki
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  8. Kenji Nohara
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Correspondence to Kenji Nohara.

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Higashi, R., Sakuma, K., Chiba, S.N. et al. Species and lineage identification for yellowfin Thunnus albacares and bigeye T. obesus tunas using two independent multiplex PCR assays. Fish Sci 82, 897–904 (2016). https://doi.org/10.1007/s12562-016-1027-3

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  • DOI: https://doi.org/10.1007/s12562-016-1027-3

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