Skip to main content
SpringerLink
Log in

Complete mitochondrial genome of the Pleuronichthys lighti (Pleuronectiformes, Pleuronectidae) with phylogenetic consideration

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

Mitochondrial genome has been used to shed light on many fields of both basic and applied research, including the study of molecular evolution. The complete mitochondrial genome sequence of 17368 bp nucleotides from the Pleuronichthys lighti was determined. It was a circular double-stranded DNA molecule with identical set of 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes as well as a non-coding control region. Stand asymmetry in the nucleotide composition was reflected in the codon usage of genes oriented in opposite directions. In the control region, we identified the extended termination associated sequence domain, the central conserved sequence block domain and the conserved sequence block domain, and two complete repeat region. They were “TTACAATA” and “TGTTGTAA”, respectively. All known 12 mitochondrial genomes of Pleuronectinae fishes were downloaded and analyzed; there were 5570 variable sites in the consensus sequences of 15241 base pairs, calculation of total sites were 35.5%. The highest sequence divergence was 50% (ATP8) and the Kimura-2-parameter genetic distance was 0.235 (ND6), whereas the COIII had the lowest sequence divergence (28.8%) and genetic distance (0.128); the protein coding genes were mainly acted by purifying selection which was detected by selection tests. Analysis of confidence and the information content for per nucleotide revealed ND5, ATP6, COI and ND4 genes were suitable molecular markers for phylogenetic study of Pleuronectinae fishes. Phylogenetic analysis using Bayesian computational algorithms based on COI genes provided support for the taxonomic status of P. lighti, which was consistent with the traditional taxonomy.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Anderson S, De Bruijn MHL, Coulson AR, Eperon IC, Sanger F, Young IG (1982) Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome. J Mol Biol 156:683–717

    Article  CAS  PubMed  Google Scholar 

  • Barr CM, Neiman M, Taylor DR (2005) Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. New Phytol 168:39–50

    Article  CAS  PubMed  Google Scholar 

  • Berendzen PB, Dimmick WW (2002) Phylogenetic relationships of Pleuronectiformes based on molecular evidence. Copeia 3:642–652

    Article  Google Scholar 

  • Broughton RE, Milam JE, Roe BA (2001) The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 11:1958–1967

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brown WM (1983) Evolution of animal mitochondrial DNA. Evol Genes Proteins 1: 62–88

    Google Scholar 

  • Chen N, Lai XP (2010) Mitochondrial genome evolution in metazoan: origin, size and gene arrangement. Biotechnol Lett 21:721–726

    CAS  Google Scholar 

  • Chen DG, Liu CG, Dou SZ (1992) The biology of flatfish (Pleuronectinae) in the coastal waters of China. Neth J Sea Res 29:25–33

    Article  Google Scholar 

  • Chen SJ, He CB, Mu YL, Liu WD, Zhou ZC, Gao XG, Cong LL (2008) Informative efficiencies of mitochondrial genes in phylogenetic analysis of teleostean. J Fish Sci China 15:12–21

    CAS  Google Scholar 

  • Guo YC (2009) Application analysis of mitochondrial DNA protein-coding gene among Perciformes. J Anhui Agric Sci 16:023

    Google Scholar 

  • He CB, Gao XG, Wang XM, Liu WD, Zhou ZC, Mu YL, Ge LL (2007) Structure and evolution of complete mitochondrial genome of spotted halibut Verasper variegatus. J Fish Sci China 14:584–592

    CAS  Google Scholar 

  • Hixson JE, Wong TW, Clayton DA (1986) Both the conserved stem-loop and divergent 5′-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J Biol Chem 261:2384–2390

    CAS  PubMed  Google Scholar 

  • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755

    Article  CAS  PubMed  Google Scholar 

  • Hurst LD (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet 18:486–487

    Article  PubMed  Google Scholar 

  • Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS (2007) Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): genome description and phylogenetic considerations inferred from the Cyt b and 16 S rRNA genes. Gene 396:13–27

    Article  CAS  PubMed  Google Scholar 

  • Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee JS (2004) The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene 336:147–153

    Article  CAS  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Kong X, Dong X, Zhang Y, Shi W, Wang Z, Yu Z (2009) A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion. Genome 52:975–984

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinformatics 9:299–306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu JX, Gao TX, Wu SF, Zhang YP (2007) Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Mol Ecol 16:275–288

    Article  CAS  PubMed  Google Scholar 

  • McMillan WO, Palumbi SR (1997) Rapid rate of control-region evolution in Pacific butterfly fishes (Chaetodontidae). J Mol Evol 45:473–484

    Article  CAS  PubMed  Google Scholar 

  • Meyer A (1994) DNA technology and phylogeny of fish. In: Beaumont AR (eds) Genetics and evolution of aquatic organisms. Chapman and Hall, London, pp 219–249

    Google Scholar 

  • Miya M, Nishida M (2000) Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol Phylogenet Evol 17:437–455

    Article  CAS  PubMed  Google Scholar 

  • Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Shirai SM (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121–138

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Pardo BG, Machordom A, Foresti F, Porto-Foresti F, Azevedo MF, Bañon R, Martínez P (2005) Phylogenetic analysis of flatfish (Order Pleuronectiformes) based on mitochondrial 16s rDNA sequences. Sci Mar 69:531–543

    Article  CAS  Google Scholar 

  • Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41:353–358

    Article  CAS  PubMed  Google Scholar 

  • Ponce M, Infante C, Jiménez-Cantizano RM, Pérez L, Manchado M (2008) Complete mitochondrial genome of the blackspot seabream, Pagellus bogaraveo (Perciformes: Sparidae), with high levels of length heteroplasmy in the WANCY region. Gene 409:44–52

    Article  CAS  PubMed  Google Scholar 

  • Rand DM (1993) Endotherms, ectotherms, and mitochondrial genome-size variation. J Mol Evol 37:281–295

    Article  CAS  PubMed  Google Scholar 

  • Sakamoto K (1984) Interrelationships of the family Pleuronectidae (Pisces: Pleuronectiformers). Mem Fac Fish Hokkaido Univ 31: 95–215

    Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F (1988) Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens-a review on the considerable within species diversity. Nucleic Acids Res 16:8207–8211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen X, Ren J, Cui Z, Sha Z, Wang B, Xiang J, Liu B (2007) The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene 403:98–109

    Article  CAS  PubMed  Google Scholar 

  • Singh VK, Mangalam AK, Dwivedi S, Naik S (1998) Primer premier: program for design of degenerate primers from a protein sequence. BioTech 24:318–319

    CAS  Google Scholar 

  • Suzuki S, Kawashima T, Nakabo T (2009) Taxonomic review of East Asian Pleuronichthys (Pleuronectiformes: Pleuronectidae), with description of a new species. Ichthyol Res 56: 276–291

    Article  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tinti F, Colombari A, Vallisneri M, Piccinetti C, Stagni AM (1999) Comparative analysis of a mitochondrial DNA control region fragment amplified from three Adriatic flatfish species and molecular phylogenesis of Pleuronectiformes. Mar Biotechnol 1:20–24

    Article  CAS  PubMed  Google Scholar 

  • Wang YJ, Tabeta O, Ren Y (1999) Age and growth of the finspotted flounder Pleuronichthys sp. in the East China Sea. J Ocean Univ Qingdao 29:604–610

    Google Scholar 

  • Wu H (1929) Study of the fishes of Amoy, part 1. Contr Biol Lab Sci Soc China 5: 1–90

    Google Scholar 

  • Xiao WH, Zhang YP (2000) Genetics and evolution of mitochondrial DNA in fish. Acta Hydrobiol Sin 24:384–391

    CAS  Google Scholar 

  • Yokogawa K, Ogihara G, Watanabe KI (2014) Identity of the lectotype of the East Asian flatfish Pleuronichthys cornutus (Temminck and Schlegel, 1846) and reinstatement of Pleuronichthys lighti Wu 1929. Ichthyol Res 61: 385–392

    Article  Google Scholar 

  • Yokogawa K, Watanabe KI, Ogihara G (2016) Redescriptions of two closely related East Asian flatfish species of the genus Pleuronichthys. Zootaxa 4205:1–23

    Article  Google Scholar 

  • Zardoya R, Meyer A (1996) Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol Biol Evol 13:933–942

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Zhang Y, Gao TX, Li PF, Xu HX (2011a) Genetic identification of two species of Pleuronichthys by DNA barcoding. Chin J Oceanol Limnol 29:967–972

    Article  CAS  Google Scholar 

  • Zhang H, Gao TX, Xu HX, Li PF (2011b) A new record of Pleuronichthys in China: Pleuronichthys japonicus. Period Ocean Univ China 41: 51–54

    CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to Mr. Zhengsen Yu and Ms. Nan Zhang for offering technical assistance during the paper writing. We also would like to acknowledge Ms. Lu Liu and Mr. Yuman Ju who expressed their opinions on drafts of this manuscript. Thanks Shah Syed Babar Hussain (Ali) for the language assistance. This study was supported by the National Natural Science Foundation of China (No. 41776171), Public Science and Technology Research Funds Projects of Ocean (201505001) and the Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhoushan (2016 KE004).

Author information

Authors and Affiliations

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

    Yaoxuan Song & Na Song

  2. Key Laboratory for Technology Research on Sustainable Utilization of Marine Fishery Resources, Marine Fisheries Research Institute of Zhejiang, Zhoushan, China

    Yongdong Zhou, Pengfei Li & Tianxiang Gao

  3. College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China

    Shujiang Zhao & Tianxiang Gao

Authors
  1. Yaoxuan Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Na Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yongdong Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pengfei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shujiang Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Tianxiang Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Shujiang Zhao or Tianxiang Gao.

Ethics declarations

Conflict of interest

Yaoxuan Song, Na Song, Yongdong Zhou, Pengfei Li, Shujiang Zhao and Tianxiang Gao declare that they have no conflict of interest.

Research involving human and animal participants

This article does not contain any studies with human subjects by any of the authors. The animal experiment throughout the study was conducted according to the Chinese Ministry of Science and Technology Guiding Directives for Humane Treatment of Laboratory Animals.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Song, Y., Song, N., Zhou, Y. et al. Complete mitochondrial genome of the Pleuronichthys lighti (Pleuronectiformes, Pleuronectidae) with phylogenetic consideration. Genes Genom 39, 1271–1284 (2017). https://doi.org/10.1007/s13258-017-0570-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-017-0570-3

Keywords

Search

Navigation