Fisheries Science

, Volume 72, Issue 5, pp 1054–1065

Complete mitochondrial DNA sequence of Atlantic horse mackerel Trachurus trachurus and molecular identification of two commercially important species T. trachurus and T. japonicus using PCR-RFLP

Article

Abstract

To characterize and identify mitochondrial DNA (mtDNA) nucleotide sequence variation in two commercially important Trachurus species, Trachurus trachurus and T. japonicus, the complete mtDNA sequence of T. trachurus was determined. The T. trachurus mtDNA consists of 16 559 bp, containing 22 transfer RNA (tRNA) genes, two rRNA genes, and 13, protein-coding genes. Comparing the mtDNA nucleotide sequences of the Trachurus species, a polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method was developed to differentiate these two commercially important species. The primer pair Lt1-ND5 and Ht1-ND5, corresponding to ND5, was designed to amplify a 360-bp fragment. Following digestion with Eco RI, the PCR product for T. japonicus resulted in 93- and 267-bp fragments, while T. trachurus lacked a restriction site for Eco RI. In contrast, after digestion with Hin fl, the T. trachurus PCR product yielded 44-, 84-, and 232-bp fragments, while the T. japonicus product was not digested. The PCR-RFLP analysis established in the present study was useful for identifying T. trachurus and T. japonicus.

Key words

Atlantic horse mackerel food labeling mitochondrial DNA RFLP species identification Trachurus trachurus 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Nichols JT. A key to the species of Trachurus. Bull. Am. Mus. Nat. Hist. 1920; 42: 477–481.Google Scholar
  2. 2.
    Chow S, Inoue S. Intra- and inter-specific restriction fragment length polymorphism in mitochondrial genes of Thunnus tuna species. Bull. Natl. Res. Inst. Far Seas Fish 1993; 30: 619–627.Google Scholar
  3. 3.
    Ram JL, Ram ML, Baidoun FF. Authentication of canned tuna and bonito by sequence and restriction site analysis of polymerase chain reaction products of mitochondrial DNA. J. Agric. Food Chem. 1996; 44: 2460–2467.CrossRefGoogle Scholar
  4. 4.
    Wakao T, Hikida Y, Tsuneyoshi T, Kaji S, Kubota H, Kubota T. A simple DNA analysis for identifyingeel species by using the polymerase chain reaction-restriction fragment length polymorphism method. Nippon Suisan Gakkaishi 1999; 65: 391–399 (in Japanese).Google Scholar
  5. 5.
    Cespedes A, Garcia T, Carrera E, Gonzalez I, Sanz B, Hernandez PE, Martin R. Polymerase chain reaction-restriction fragment length polymorphism analysis of a short fragment of the cytochrome b gene for identification of flatfish species. J. Food Prot. 1998; 61: 1684–1685.PubMedGoogle Scholar
  6. 6.
    Russell VI, Hold GL, Pryde SE, Rehbein H, Quinteiro J, Rey-Méndez M, Sotelo CG, Perez-Martin R, Santos AT, Rosa C. Use of restriction fragment length polymorphism to distinguish between salmon species. J. Agric. Food Chem. 2000; 48: 2148–2188.CrossRefGoogle Scholar
  7. 7.
    Sotelo CG, Calo-Mata P, Chapela MJ, Perez-Martin RI, Rehbein H, Hold GL, Russell VJ, Pryde S, Quinteiro J, Izquierdo M, Rey-Méndez M, Rosa C, Santos AT. Identification of flatfish (Pleuronectiform) species using DNA-based techniques. J. Agric. Food Chem. 2001; 49: 4562–4569.PubMedCrossRefGoogle Scholar
  8. 8.
    Takeyama H., Chow S, Tsuzuki H, Matsunaga T. Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification. J. Fish Biol. 2001; 58: 1646–1657.CrossRefGoogle Scholar
  9. 9.
    Hold GL, Russell VJ, Pryde SE, Rehbein H, Quinteiro J, Vidal R, Rey-Méndez M, Sotelo CG, Perez-Martin RI, Santos AT, Rosa C. Development of a DNA-based method aimed at identifying the fish species present in food products. J. Agric. Food Chem. 2001; 49: 1175–1179.PubMedCrossRefGoogle Scholar
  10. 10.
    Jerome M, Lemaire K, Verrez-Bagnis V, Etienne M. Molecular phylogeny and species identification of sardines. J Agric. Food Chem. 2003; 51: 43–50.PubMedCrossRefGoogle Scholar
  11. 11.
    Chow S, Nohara K, Tanabe T, Itoh T, Tsuji S, Nishikawa Y, Uyeyanagi S, Uchikawa K. 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. Agen. 2003; 8: 1–14.Google Scholar
  12. 12.
    Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.Google Scholar
  13. 13.
    Miya M, Nishida M. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogent. Evol. 2000; 17: 437–455.CrossRefGoogle Scholar
  14. 14.
    Morita T. Molecular phylogenetic relationships of the deep-sea fish genus Coryphaenoides (Gadiformes: Macrouridae) based on mitochondrial DNA. Mol. Phylogenet. Evol. 1999; 13: 447–454.PubMedCrossRefGoogle Scholar
  15. 15.
    Reed DL, de Gravelle MJ, Carpenter KE. Molecular systematics of Selene (Perciformes: Carangidae) based on cytb sequences. Mol. Phylogenet. Evol. 2001; 21: 468–475.PubMedCrossRefGoogle Scholar
  16. 16.
    Bartlett SE, Davidson WS. FINS (forensically informative nucleotide sequencing): a procedure for identifying the antimal origin of biological specimens. Biotechniques 1992; 13: 408–411.Google Scholar
  17. 17.
    Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlichi DP, Roe BA, Sanger F, Schrier PH, Smith AJH, Staden R, Young IG. Sequence and organization of the human mitochondrial genome. Nature 1981; 290: 457–465.PubMedCrossRefGoogle Scholar
  18. 18.
    Anderson S, de Bruijn MHL, Coulson AR, Eperon IC, Sanger F, Young IG. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 1982; 156: 683–717.PubMedCrossRefGoogle Scholar
  19. 19.
    Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA. Sequence and gene organization of mouse mitochondrial DNA. Cell 1981; 26: 167–180.PubMedCrossRefGoogle Scholar
  20. 20.
    Roe BA, Ma DP, Wilson RK, Wong JF. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 1985; 260: 9759–9774.PubMedGoogle Scholar
  21. 21.
    Inoue GJ, Miya M, Tsukamoto K, Nishida M. Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish. Sci. 2000; 66: 924–932.CrossRefGoogle Scholar
  22. 22.
    Inoue GJ, Miya M, Aoyama J, Ishikawa S, Tsukamoto K, Nishida M. Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica. Fish. Sci. 2001; 67: 118–125.CrossRefGoogle Scholar
  23. 23.
    Ishiguro N, Miya M, Nishida M. Complete mitochondrial DNA sequence of ayu Plecoglossus altivelis. Fish. Sci. 2001; 67: 474–481.CrossRefGoogle Scholar
  24. 24.
    Inoue GJ, Miya M, Tsukamoto K, Nishida M. Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus. Fish. Sci. 2001; 67: 828–835.CrossRefGoogle Scholar
  25. 25.
    Cardenas L, Hernandez CE, Poulin E, Magoulas A, Kornfield I, Ojeda FP. Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae). Mol. Phylogenet. Evol. 2005; 35: 496–507.PubMedCrossRefGoogle Scholar
  26. 26.
    Karaiskou N, Triantafyllidis A, Triantaphllidis C. Discrimination of three Trachurus species using both mitochondrial-and nuclear-based DNA approaches. J. Agric. Food Chem. 2003; 51: 4935–4940.PubMedCrossRefGoogle Scholar
  27. 27.
    Gadaleta G, Pepe G, Candia DG, Quagliariello C, Sbisa E, Saccone C. Nucleotide sequence of rat mitochondrial NADH dehydrogenase subunit. 1. GTG, a new initiator codon in vertebrate mitochondrial genome. Nucleic Acids Res. 1988; 16: 6233.PubMedCrossRefGoogle Scholar
  28. 28.
    Johansen S, Guddal HP, Johansen T. Organization of the mitochondrial genome of Atlantic cod, Gadus morhua. Nucleic Acids Res. 1990; 18: 411–419.PubMedCrossRefGoogle Scholar

Copyright information

© The Japanese Society of Fisheries Science 2006

Authors and Affiliations

  1. 1.National Research Institute of Fisheries ScienceFukuura, YokohamaJapan
  2. 2.Center for Food QualityLabeling and Consumer Services HeadquarterShintoshin, SaitamaJapan

Personalised recommendations