Skip to main content
Springer Nature Link
Log in

Complete nucleotide sequences of mitochondrial DNA of long-finned squid Loligo edulis

  • Original Article
  • Biology
  • Published:
Fisheries Science Aims and scope Submit manuscript

Abstract

The complete nucleotide sequence of the mitochondrial genome of long-finned squid Loligo edulis forma kensaki (L. edulis f. kensaki, Teuthida: Myopsida) was determined. It contains 13 protein-coding genes, 12SrRNA, 16SrRNA, and the 22 tRNA genes, and three long noncoding regions. We also determined the mitochondrial genome nucleotide sequence of seasonal brood samples of L. edulis f. budo collected from the western part of the Sea of Japan in the autumn to winter seasons, which showed morphologic discrepancies with L. edulis f. kensaki. Comparison of the two complete sets of mitochondrial DNA data showed that the similarity of the two sequences was as high as 99.9 %, with only eight nucleotide substitutions in coding regions. The complete mitochondrial genome of Loligo edulis f. kensaki from Nagasaki Pref. is 17360 bp and L. edulis f. budo from the Shimane Pref. is 17351 bp. The nucleotide sequences and haplotype patterns in ND1 suggest that L. edulis f. kensaki and L. edulis f. budo share a single genetic background.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Boletzky SV (2003) Biology of early life stages in cephaolopod molluscs. Adv Mar Biol 44:143–203

    Article  Google Scholar 

  2. Statistics Department of Ministry of Agriculture, Forestry and Fisheries (2010) Annual statistics of fishery and fish culture. Association of Agriculture and Forestry Statistics, Tokyo

    Google Scholar 

  3. Ministry of Finance Japan (2011) Trade statistics of Japan. Ministry of Finance, Tokyo

  4. Ikehara K, Kasahara S, Okachi I, Shimizu T, Hamabe M (1977) Ecology and maturity process in Loligo edulis budo Wakiya et Ishikawa fished in the waters around the Oki islets in the Western Japan Sea. Bull Jap Sea Reg Fish Res Lab 28:29–49

    Google Scholar 

  5. Shimizu T, Hoshino S (1991) On the Loliginid Squid, Loligo edulis, Resources in the Eastern China Sea. Bull Kanagawa Pref Fish Exp Stn 12:65–72

    Google Scholar 

  6. Roper CFE, Swwney MJ, Nauen CE (1984) Cephalopods of the world, an annotated illustrated catalogue of species of interest to fisheries. FAO Fish Synop 3:1–277

    Google Scholar 

  7. Bonnaud L, Boucher-Rodoni R, Monnerot M (1996) Relationship of some coleoid cephalopods established by 3′ end of the 16SrRNA and cytochrome oxidase III gene sequence comparison. Am Malacol Bull 12:87–90

    Google Scholar 

  8. Bonnaud L, Boucher-Rodoni R, Monnerot M (1997) Phylogeny of cephalopods inferred from mitochondrial DNA sequences. Mol Phyl Evol 7:44–54

    Article  CAS  Google Scholar 

  9. Takumiya M, Kobayashi M, Tsuneki K, Furuya H (2005) Phylogenetic relationships among major species of Japanese coleoid cephalopods (Mollusca: Cephalopoda) using three mitochondrial DNA sequences. Zool Sci 22:147–155

    Article  PubMed  CAS  Google Scholar 

  10. Tomita K, Yokobori S, Oshima T, Ueda T, Watanabe K (2002) The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes. J Mol Evol 54:486–500

    Article  PubMed  CAS  Google Scholar 

  11. Okutani T (1978) Stock assessment of cephalopod resources fished by Japan. FAO Fish Tech Paper 173:69

    Google Scholar 

  12. Okutani T (2005) Cuttlefishes and squids of the world (in Japanese). Seizando-Shoten, Tokyo, pp 104–105

    Google Scholar 

  13. Natsukari Y, Nishiyama Y, Nakanishi Y (1986) A preliminary study on the isozymes of the loliginid squid Photololigo edulis (Hoyle, 1885). Rep Coop Invest “Shiro-Ika” Loligo edulis Inhab W Jpn Sea 2:145–151 (in Japanese with English abstract)

  14. Natsukari Y, Nakanose T, Oda K (1988) Age and growth of the loliginid squid Photololigo edulis (Hoyle, 1885). J Exp Mar Biol Ecol 116:177–190

    Article  Google Scholar 

  15. Natsukari Y, Tashiro M (1991) Neritic squid resources and cuttlefish resources in Japan. Mar Behav Physiol 18:149–226

    Article  Google Scholar 

  16. Natsukari Y (1995) The elucidation of the actual condition of Loligo edulis kensaki and Loligo edulis budo. In: Ika No Syunjyu. Seizando-Shoten, Tokyo, pp 31–37

  17. Aoki M, Imai H, Naruse T, Ikeda Y (2008) Low genetic diversity of oval squid, Sepioteuthis cf. lessoniana (Cephalopoda: loliginidae), in Japanese waters inferred from a mitochondrial DNA non-coding region. Pac Sci 62:403–411

    Article  CAS  Google Scholar 

  18. Herke SW, Foltz DW (2002) Phylogeography of two squid (Loligo pealei and L. plei) in the Gulf of Mexico and northwestern Atlantic Ocean. Mar Biol 140:103–115

    Article  CAS  Google Scholar 

  19. Ito K, Yanagimoto T, Iwata Y, Munehara H, Sakurai Y (2006) Genetic population structure of the spear squid Loligo bleekeri based on mitochondrial DNA (in Japanese with English abstract). Nippon Suisan Gakkaishi 72:905–910

    Article  CAS  Google Scholar 

  20. Shaw PW, Arkhipkin AI, Adcock GJ, Burnett WJ, Carvalho GR, Scherbich JN, Villegas PA (2004) DNA markers indicate that distinct spawning cohorts and aggregations of Patagonian squid, Loligo gahi, do not represent genetically discrete subpopulations. Mar Biol 144:961–970

    Article  CAS  Google Scholar 

  21. Shaw PW, Pierce GJ, Boyle PR (1999) Subtle population structuring within a highly vagile marine invertebrate, the veined squid Loligo forbesi, demonstrated with microsatellite DNA markers. Mol Ecol 8:407–417

    Article  CAS  Google Scholar 

  22. Yamashita M, Namikoshi A, Iguchi J, Takashima Y, Hossain MA, Yabu T, Yamashita Y (2008) Molecular identification of species and the geographic origin of seafood. In: Tsukamoto K, Kawamura T, Takeuchi T, Beard TD Jr, Kaiser MJ (eds) Fisheries for global welfare and environment (Memorial Book of the 5th World Fisheries Congress). Terrapub, Tokyo, pp 279–306

  23. Iguchi J, Takashima Y, Namikoshi A, Yamashita M (2012) Species identification method for marine products of Seriola and related species. Fish Sci 78:197–206

    Article  CAS  Google Scholar 

  24. Namikoshi A, Takashima Y, Iguchi J, Yanagimoto T, Yamashita M (2011) Species identification of Alaska pollock, Gadus spp., and Micromesistius spp. in cod roe products using a PCR-based method. Fish Sci 77:671–678

    Article  CAS  Google Scholar 

  25. Santaclara FJ, Espineira M, Vieites JM (2007) Genetic identification of squids (families Ommastrephidae and Loliginidae) by PCR–RFLP and FINS methodologies. J Agric Food Chem 55:9913–9920

    Article  PubMed  CAS  Google Scholar 

  26. Yanagimoto T, Kitamura T (2002) Identification of three gadoid species around Hokkaido using the mitochondrial cytochrome b gene (in Japanese with English abstract). Nippon Suisan Gakkaishi 68:893–899

    Article  CAS  Google Scholar 

  27. Yanagimoto T (2003) Identification of seven greenling species using polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis of mitochondrial DNA (in Japanese with English abstract). Nippon Suisan Gakkaishi 69:726–732

    Article  CAS  Google Scholar 

  28. Yanagimoto T (2007) Identification of three atelecyclid crab species (Decapoda: Crustacea) by SSP-PCR analysis (in Japanese with English abstract). Nippon Suisan Gakkaishi 73:872–879

    Article  CAS  Google Scholar 

  29. Takashima Y, Morita T, Yamashita M (2005) Complete mitochondrial DNA sequence of Atlantic horse mackerel Trachurus trachurus and molecular identification of two commercially important species T. trachurus and T. japonicas using PCR–RFLP. Fish Sci 71:414–421

    Article  Google Scholar 

  30. Sambrook J, Fritsh EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  31. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5436–5467

    Article  Google Scholar 

  32. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 24:4876–4882

    Article  Google Scholar 

  33. Nei M, Tajima F (1981) DNA polymorphism detected by restriction endonucleases. Genetics 97:145–163

    PubMed  CAS  Google Scholar 

  34. Excoffier L, Lischer HEL (2010) Arlequin suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

  35. Weir BS, Cockerman CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  36. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619–633

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Dr. Hidetaka Furuya for providing the DNA samples.

Author information

Authors and Affiliations

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

    Kenji Takemoto & Michiaki Yamashita

Authors
  1. Kenji Takemoto
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Michiaki Yamashita
    View author publications

    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence to Michiaki Yamashita.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Takemoto, K., Yamashita, M. Complete nucleotide sequences of mitochondrial DNA of long-finned squid Loligo edulis . Fish Sci 78, 1031–1039 (2012). https://doi.org/10.1007/s12562-012-0541-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12562-012-0541-1

Keywords