Thanks to visit codestin.com
Credit goes to link.springer.com

Skip to main content
Springer Nature Link
Log in

Complete mitogenome sequence of black carp (Mylopharyngodon piceus) and its use for molecular phylogeny of leuciscine fishes

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

The black carp Mylopharyngodon piceus (Cyprinidae), native to eastern Asian, is a large, commercially important fish, and has been introduced to many other countries for variable reasons. In this study, the complete mitochondrial genome sequences from three specimens of black carp were first determined and were used to evaluate the sister relationship between black carp and grass carp (Ctenopharyngodon idellus). Two individuals had a mitogenome of 16,609 bp, while the other was 16,611 bp in length. Similar to most vertebrates, the black carp contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analyses using three different computational algorithms (Maximum Parsimony, Maximum Likelihood, and Bayesian analysis) revealed two distinct clades in subfamily Leuciscinae. However, the sister taxonomic relationship of black carp and grass carp was not observed using sequences of nearly complete mitochondrial genomes, which suggests more nuclear gene markers are needed to resolve the phylogenetic relationship between black carp and grass carp.

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+
from £29.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Explore related subjects

Discover the latest articles, books and news in related subjects, suggested using machine learning.

References

  1. Li SZ, Fang F (1990) On the geographical distribution of the four kinds of pond-cultured carps in China. Acta Zool Sinica 36:244–248 (In Chinese with English abstract)

    Google Scholar 

  2. Chen YY (1998) Fauna Sinica, Osteichthyes, Cypriniformes II. Science Press, Beijing, pp 1–16

    Google Scholar 

  3. Li SF (1998) Genetic characterization of major freshwater culture fishes in China. Shanghai Scientific & Technical Publishers, Shanghai, pp 142–147

    Google Scholar 

  4. Ben-Ami F, Heller J (2001) Biological control of aquatic pest snails by the black carp, Mylopharyngodon piceus. Biol Cont 22:131–138

    Article  Google Scholar 

  5. Nico LG, Williams JD, Jelks HL (2005) Black carp: biological synopsis and risk assessment of an introduced fish. American Fisheries Society, Bethesda, p 337

    Google Scholar 

  6. Nelson JS (2006) Fishes of the world, 4th edn. Wiley, Hoboken, p 142

    Google Scholar 

  7. He S, Liu H, Chen Y, Kuwahara M, Nakajima T, Zhong Y (2004) Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences. Sci China Ser C Life Sci 47:130–138

    Article  CAS  Google Scholar 

  8. Wang X, Li J, He S (2007) Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol 42:157–170

    Article  PubMed  CAS  Google Scholar 

  9. He S, Mayden RL, Wang X, Wang W, Tang KL, Chen W, Chen Y (2008) Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family. Mol Phylogenet Evol 46:818–829

    Article  PubMed  CAS  Google Scholar 

  10. Tao W, Zou M, Wang X, Gan X, Mayden RL, He S (2010) Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes). PLoS ONE 5:e13508

    Article  PubMed  Google Scholar 

  11. Howes GJ (1981) Anatomy and phylogeny of the Chinese major carps Ctenopharyngodon Steind., 1866 and Hypophthalmichthys Blkr, 1860. Bull Br Mus (Nat Hist) Zool 41:1–52

    Google Scholar 

  12. Avise JC (1994) Molecular marker, natural history and evolution. Chapman & Hall, New York

    Book  Google Scholar 

  13. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge

    Google Scholar 

  14. Boore J (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780

    Article  PubMed  CAS  Google Scholar 

  15. Yue G, Liew W, Orban L (2006) The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae). BMC Genom 7:242

    Article  Google Scholar 

  16. Zhu ZY, Yue GH (2008) The complete mitochondrial genome of red grouper Plectropomus leopardus and its applications in identification of grouper species. Aquaculture 276:44–49

    Article  CAS  Google Scholar 

  17. Catanese G, Infante C, Manchado M (2008) Complete mitochondrial DNA sequences of the frigate tuna Auxis thazard and the bullet tuna Auxis rochei. DNA Seq 19:159–166

    Article  PubMed  CAS  Google Scholar 

  18. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S (2008) Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae. Gene 424:96–101

    Article  PubMed  CAS  Google Scholar 

  19. Peng Z, Wang J, He S (2006) The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376:290–297

    Article  PubMed  CAS  Google Scholar 

  20. Catanese G, Manchado M, Infante C (2010) Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species. Gene 452:35–43

    Article  PubMed  CAS  Google Scholar 

  21. Jondeung A, Karinthanyakit W (2010) The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21:36–47

    Article  PubMed  CAS  Google Scholar 

  22. Sambrook Jl, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York, pp 479–483

    Google Scholar 

  23. Chang YS, Huang FL, Lo TB (1994) The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 38:138–155

    Article  PubMed  CAS  Google Scholar 

  24. Mabuchi K, Miya M, Senou H, Suzuki T, Nishida M (2006) Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): further evidence for an ancient origin. Aquaculture 257:68–77

    Article  CAS  Google Scholar 

  25. Murakami M, Yamashita Y, Fujitani H (1998) The complete sequence of mitochondrial genome from a gynogenetic triploid “ginbuna” (Carassius auratus langsdorfi). Zool Sci 15:335–337

    Article  PubMed  CAS  Google Scholar 

  26. Saitoh K, Sado T, Mayden R, Hanzawa N, Nakamura K, Nishida M, Miya M (2006) Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826–841

    Article  PubMed  CAS  Google Scholar 

  27. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid Symp Ser 41:95–98

    CAS  Google Scholar 

  28. Ojala D, Merkel C, Gelfand R, Attardi G (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 22:393–403

    Article  PubMed  CAS  Google Scholar 

  29. 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  PubMed  CAS  Google Scholar 

  30. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  CAS  Google Scholar 

  31. Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4:18

    Article  PubMed  Google Scholar 

  32. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793–808

    Article  PubMed  Google Scholar 

  33. Posada D (2008) jModeltest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256

    Article  PubMed  CAS  Google Scholar 

  34. Li SF, Xu JW, Yang QL, Wang CH, Chen Q, Chapman DC, Lu G (2009) A comparison of complete mitochondrial genomes of silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis: implications for their taxonomic relationship and phylogeny. J Fish Biol 74:1787–1803

    Article  PubMed  CAS  Google Scholar 

  35. 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 16S rRNA genes. Gene 396:13–27

    Article  PubMed  CAS  Google Scholar 

  36. 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

    PubMed  CAS  Google Scholar 

  37. He AY, Lou YJ, Yang H, Liu LP, Li SF, Wang CH (2011) Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Mol Biol Rep 38:2015–2021

    Article  PubMed  CAS  Google Scholar 

  38. Galtier N, Nabholz B, Glemin S, Hurst GDD (2009) Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol 18:4541–4550

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors are grateful to Minghu Tang and Lixia Fu for their help with fish collections. Meanwhile, the authors want to express special thanks to the reviewers for their valuably constructive comments. The work was supported by the National Natural Science Foundation of China (Grant No. 30630051) and the Shanghai Leading Academic Discipline project (Grant No. Y1101).

Author information

Authors and Affiliations

  1. Key Laboratory of Aquatic Genetic Resources and Utilization Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China

    Chenghui Wang, Jun Wang, Jinquan Yang, Xiao Song, Qin Chen, Jiawei Xu, Qinling Yang & Sifa Li

  2. Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA

    Guoqing Lu

Authors
  1. Chenghui Wang
    View author publications

    Search author on:PubMed Google Scholar

  2. Jun Wang
    View author publications

    Search author on:PubMed Google Scholar

  3. Jinquan Yang
    View author publications

    Search author on:PubMed Google Scholar

  4. Guoqing Lu
    View author publications

    Search author on:PubMed Google Scholar

  5. Xiao Song
    View author publications

    Search author on:PubMed Google Scholar

  6. Qin Chen
    View author publications

    Search author on:PubMed Google Scholar

  7. Jiawei Xu
    View author publications

    Search author on:PubMed Google Scholar

  8. Qinling Yang
    View author publications

    Search author on:PubMed Google Scholar

  9. Sifa Li
    View author publications

    Search author on:PubMed Google Scholar

Corresponding authors

Correspondence to Chenghui Wang or Guoqing Lu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 89 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, C., Wang, J., Yang, J. et al. Complete mitogenome sequence of black carp (Mylopharyngodon piceus) and its use for molecular phylogeny of leuciscine fishes. Mol Biol Rep 39, 6337–6342 (2012). https://doi.org/10.1007/s11033-012-1455-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1007/s11033-012-1455-9

Keywords