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Determination of the complete mitochondrial DNA sequence of Octopus minor

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Abstract

In this study, we have determined the complete nucleotide sequence of the mitochondrial genome of Octopus minor. It is 15,974 nucleotide pairs and encodes 13 proteins, two ribosomal RNAs and 22 tRNAs of the mitochondrion’s own protein synthesizing system. Seven of thirteen proteins are encoded by the H-strand, while the other six proteins, as well as the two ribosomal RNAs are encoded by the L-strand. The nucleotide composition of the proteins showed a nucleotide bias against G encoded by the H-strand, while they showed a nucleotide bias against A and C encoded by the L-strand. Two of the 13 protein coding genes of O. minor began with the unorthodox translation initiation codon ATA and all others use the standard ATG. In addition, six of thirteen mt proteins of O. minor have unambiguous termination codons. There are four cases where tRNA genes appear to overlap. The long noncoding region (LNCR) of O. minor was 930 nucleotides and no repeated sequences were found in this LNCR. The gene arrangements of O. minor showed remarkable similarity to that of O. ocellatus and O. vulgaris. Phylogenetic analysis demonstrated that O. minor appears as sister taxan to the monophyletic group combined by O. ocellatus and O. vulgaris, suggesting a relative distant genetic relationship between O. minor and the other two octopus species.

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References

  1. Boyle PR, Rodhouse P (2005) Cephalopods: ecology and fisheries. Blackwell, London

    Google Scholar 

  2. Nesis KN (1998) Biodiversity and systematics in cephalopods: unresolved problems require an integrated approach. S Afr J Marine Sci 20(1):165–173

    Article  Google Scholar 

  3. Norman MD, Sweeney MJ (1997) The shallow-water octopuses (Cephalopoda: Octopodidae) of the Philippines. Invertebr Taxon 11(1):89–140

    Article  Google Scholar 

  4. Voight JR (1994) Morphological variation in shallow-water octopuses (Mollusca, Cephalopoda). J Zool 232:491–504

    Article  Google Scholar 

  5. Roper CFE, Hochberg FG (1998) Behavior and systematics of cephalopods from Lizard Island, Australia, based on color and body patterns. Malacol 29(1):153–194

    Google Scholar 

  6. Boore JL (1999) Animal mitochondrial genomes. Nucl Acids Res 27(8):1767–1780

    Article  PubMed  CAS  Google Scholar 

  7. Hoffmann RJ, Boore JL, Brown WM (1992) A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131(2):397–412

    PubMed  CAS  Google Scholar 

  8. Xu K, Kanno M, Yu H, Li Q, Kijima A (2011) Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys farreri (Bivalvia: Pectinidae). Mol Biol Rep 38(5):3067–3074

    Google Scholar 

  9. Zheng X, Li Q, Wang Z, Yu R, Tian C, Wang R (2005) Genetic diversity in populations of Sepiella japonica based on the mitochondrial DNA sequence analysis. Phuket Mar Bio Cent Res Bull 66:195–201

    Google Scholar 

  10. Zheng X, Yang J, Lin X, Wang R (2004) Phylogenetic relationships among the decabrachia cephalopods inferred from mitochondrial DNA sequences. J Shellfish Res 23(3):881–886

    Google Scholar 

  11. Liu Y, Cui Z (2011) Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): genome characterization and phylogenetic considerations. Mol Biol Rep 38(1):403–410

    Article  PubMed  CAS  Google Scholar 

  12. Bonnaud L, Boucher-Rodoni R, Monnerot M (1994) Phylogeny of decapod cephalopods based on partial 16S rDNA nucleotide sequences. C R Acad Sci III 317(6):581–588

    PubMed  CAS  Google Scholar 

  13. Bonnaud L, Boucher-Rodoni R, Monnerot M (1997) Phylogeny of cephalopods inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 7(1):44–54

    Article  PubMed  CAS  Google Scholar 

  14. Persis M, Chandra Sekhar Reddy A, Rao LM, Khedkar GD, Ravinder K, Nasruddin K (2009) COI (cytochrome oxidase-I) sequence based studies of Carangid fishes from Kakinada coast, India. Mol Biol Rep 36(7):1733–1740

    Article  PubMed  CAS  Google Scholar 

  15. Lakra WS, Goswami M, Gopalakrishnan A (2009) Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes, Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes. Mol Biol Rep 36(5):831–839

    Article  PubMed  CAS  Google Scholar 

  16. Lydeard C, Holznagel WE, Schnare MN, Gutell RR (2000) Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures. Mol Phylogenet Evol 15(1):83–102

    Article  PubMed  CAS  Google Scholar 

  17. Liu Y, Cui Z (2010) Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods. Mol Biol Rep 37(5):2559–2569

    Article  PubMed  CAS  Google Scholar 

  18. Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173–216

    Article  PubMed  CAS  Google Scholar 

  19. Shen X, Wang H, Ren J, Tian M, Wang M (2009) The mitochondrial genome of Euphausia superba (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers. Mol Biol Rep 37(2):771–784

    Article  PubMed  Google Scholar 

  20. Boore JL, Staton JL (2002) The mitochondrial genome of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Mol Biol Evol 19(2):127–137

    Article  PubMed  CAS  Google Scholar 

  21. Helfenbein KG, Boore JL (2004) The mitochondrial genome of Phoronis architecta: comparisons demonstrate that phoronids are lophotrochozoan protostomes. Mol Biol Evol 21(1):153–157

    Article  PubMed  CAS  Google Scholar 

  22. Allcock AL, Cooke IR, Strugnell JM (2011) What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda? Zool J Linn Soc 161(3):573–586

    Article  Google Scholar 

  23. Okutani T, Tagawa M, Horikawa H (1987) Cephalopods from continental shelf and slope around Japan. Japan Fisheries Resource Conservation Association, Tokyo

    Google Scholar 

  24. Akasaki T, Nikaido M, Tsuchiya K, Segawa S, Hasegawa M, Okada N (2006) Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol Phylogenet Evol 38(3):648–658

    Article  PubMed  CAS  Google Scholar 

  25. Yokobori S, Fukuda N, Nakamura M, Aoyama T, Oshima T (2004) Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes. Mol Biol Evol 21(11):2034–2046

    Article  PubMed  CAS  Google Scholar 

  26. Simon C, Frati F, Bechenbach A, Crespi B, Liu H, Flook P (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am 87:651–701

    CAS  Google Scholar 

  27. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3(5):294–299

    PubMed  CAS  Google Scholar 

  28. Mathews DH (2006) RNA secondary structure analysis using RNAstructure. Curr Protoc Bioinformatics. 12:12.6

    Google Scholar 

  29. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599

    Article  PubMed  CAS  Google Scholar 

  30. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17(4):540–552

    PubMed  CAS  Google Scholar 

  31. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5):696–704

    Article  PubMed  Google Scholar 

  32. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21(9):2104–2105

    Article  PubMed  CAS  Google Scholar 

  33. Vallès Y, Boore JL (2006) Lophotrochozoan mitochondrial genomes. Integr Comp Biol 46(4):544–557

    Article  PubMed  Google Scholar 

  34. Rigaa A, Monnerot M, Sellos D (1995) Molecular cloning and complete nucleotide sequence of the repeated unit and flanking gene of the scallop Pecten maximus mitochondrial DNA: putative replication origin features. J Mol Evol 41(2):189–195

    Article  PubMed  CAS  Google Scholar 

  35. Fuller KM, Zouros E (1993) Dispersed discrete length polymorphism of mitochondrial DNA in the scallop Placopecten magellanicus (Gmelin). Curr Genet 23(4):365–369

    Article  PubMed  CAS  Google Scholar 

  36. Boore JL, Medina M, Rosenberg LA (2004) Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol 21(8):1492–1503

    Article  PubMed  CAS  Google Scholar 

  37. Stewart DT, Saavedra C, Stanwood RR, Ball AO, Zouros E (1995) Male and female mitochondrial DNA lineages in the blue mussel (Mytilus edulis) species group. Mol Biol Evol 12(5):735–747

    PubMed  CAS  Google Scholar 

  38. Passamonti M, Boore JL, Scali V (2003) Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarum. Genetics 164(2):603–611

    PubMed  CAS  Google Scholar 

  39. Crozier RH, Crozier YC (1993) The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 133(1):97–117

    PubMed  CAS  Google Scholar 

  40. Anderson S, Bankier AT, Barrell BG et al (1981) Sequence and organization of the human mitochondrial genome. Nature 290(5806):457–465

    Article  PubMed  CAS  Google Scholar 

  41. Bessho Y, Ohama T, Osawa S (1992) Planarian mitochondria. II. The unique genetic code as deduced from cytochrome c oxidase subunit I gene sequences. J Mol Evol 34(4):331–335

    Article  PubMed  CAS  Google Scholar 

  42. Jacobs HT, Elliott DJ, Math VB, Farquharson A (1988) Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J Mol Biol 202(2):185–217

    Article  PubMed  CAS  Google Scholar 

  43. Pont-Kingdon GA, Beagley CT, Okimoto R, Wolstenholme DR (1994) Mitochondrial DNA of the sea anemone, Metridium senile (Cnidaria): prokaryote-like genes for tRNA(f-Met) and small-subunit ribosomal RNA, and standard genetic code specificities for AGR and ATA codons. J Mol Evol 39(4):387–399

    Article  PubMed  CAS  Google Scholar 

  44. Beagley CT, Okimoto R, Wolstenholme DR (1998) The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics 148(3):1091–1108

    PubMed  CAS  Google Scholar 

  45. Clary DO, Wolstenholme DR (1985) The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol 22(3):252–271

    Article  PubMed  CAS  Google Scholar 

  46. Yokobori S, Ueda T, Watanabe K (1993) Codons AGA and AGG are read as glycine in ascidian mitochondria. J Mol Evol 36(1):1–8

    Article  PubMed  CAS  Google Scholar 

  47. Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA (1981) Sequence and gene organization of mouse mitochondrial DNA. Cell 26(2 Pt 2):167–180

    Article  PubMed  CAS  Google Scholar 

  48. Ohama T, Osawa S, Watanabe K, Jukes TH (1990) Evolution of the mitochondrial genetic code. IV. AAA as an asparagine codon in some animal mitochondria. J Mol Evol 30(4):329–332

    Article  PubMed  CAS  Google Scholar 

  49. Pont-Kingdon G, Vassort CG, Warrior R, Okimoto R, Beagley CT, Wolstenholme DR (2000) Mitochondrial DNA of Hydra attenuata (Cnidaria): a sequence that includes an end of one linear molecule and the genes for l-rRNA, tRNA(f-Met), tRNA(Trp), COII, and ATPase8. J Mol Evol 51(4):404–415

    PubMed  CAS  Google Scholar 

  50. Clary DO, Wolstenholme DR (1985) The ribosomal RNA genes of Drosophila mitochondrial DNA. Nucleic Acids Res 13(11):4029–4045

    Article  PubMed  CAS  Google Scholar 

  51. Yokobori S, Pääbo S (1995) Transfer RNA editing in land snail mitochondria. Proc Natl Acad Sci USA 92(22):10432–10435

    Article  PubMed  CAS  Google Scholar 

  52. Tomita K, Ueda T, Ishiwa S, Crain PF, McCloskey JA, Watanabe K (1999) Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria. Nucl Acids Res 27(21):4291–4297

    Article  PubMed  CAS  Google Scholar 

  53. Tomita K, Ueda T, Watanabe K (1998) 7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNA(Ser)GCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria. Biochim Biophys Acta 1399(1):78–82

    PubMed  CAS  Google Scholar 

  54. Battey J, Clayton DA (1980) The transcription map of human mitochondrial DNA implicates transfer RNA excision as a major processing event. J Biol Chem 255(23):11599–11606

    PubMed  CAS  Google Scholar 

  55. Ojala D, Montoya J, Attardi G (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature 290(5806):470–474

    Article  PubMed  CAS  Google Scholar 

  56. Yokobori S, Lindsay DJ, Yoshida M, Tsuchiya K, Yamagishi A, Maruyama T, Oshima T (2007) Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods. Mol Phylogenet Evol 44(2):898–910

    Article  PubMed  CAS  Google Scholar 

  57. Boore JL (2006) The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC genomics 7:182

    Article  PubMed  Google Scholar 

  58. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36

    PubMed  CAS  Google Scholar 

  59. Dong ZZ (1988) Fauna Sinica. Phylum Mollusca. Class Cephalopoda. Science Press, Beijing, pp 174–175, 181–184 (In Chinese)

  60. Guzik MT, Norman MD, Crozier RH (2005) Molecular phylogeny of the benthic shallow-water octopuses (Cephalopoda: Octopodinae). Mol Phylogenet Evol 37(1):235–248

    Article  PubMed  CAS  Google Scholar 

  61. Lindgren AR, Giribet G, Nishiguchi MK (2004) A combined approach to the phylogeny of Cephalopoda (Mollusca). Cladistics 20(5):454–486

    Article  Google Scholar 

  62. Strugnell J, Nishiguchi MK (2007) Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from three mitochondrial and six nuclear loci: a comparison of alignment, implied alignment and analysis methods. J Molluscan Stud 73:399–410

    Article  Google Scholar 

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Acknowledgments

This study was supported by National High Technology Research and Development Program of China (863Program) (no. 2007AA09Z433) and the National Marine Public Welfare Research Project (no. 200805069). We thank Dr. Hong Yu (Ocean University of China) for providing some reasonable advice on the manuscript. We would also like to thank Mr. Yaosen Qian (Ocean University of China) for providing us with the samples.

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Authors and Affiliations

  1. Fisheries College, Ocean University of China, Qingdao, 266003, China

    Rubin Cheng, Xiaodong Zheng & Qi Li

  2. Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China

    Rubin Cheng & Xiangzhi Lin

  3. Shandong Marine Fisheries Research Institute, Yantai, 264006, China

    Jianmin Yang

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  1. Rubin Cheng
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  2. Xiaodong Zheng
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  3. Xiangzhi Lin
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Correspondence to Xiaodong Zheng.

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Rubin Cheng, Xiaodong Zheng contributed equally to this study.

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Cheng, R., Zheng, X., Lin, X. et al. Determination of the complete mitochondrial DNA sequence of Octopus minor . Mol Biol Rep 39, 3461–3470 (2012). https://doi.org/10.1007/s11033-011-1118-2

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