Skip to main content

Complete sequence and gene organization of the mitochondrial genome of Siamensis Crocodile (Crocodylus siamensis)

Molecular Biology Reports volume 35, pages 133–138 (2008)Cite this article

Abstract

The complete sequence of mitochondrial genome of Siamensis Crocodile (Crocodylus siamensis) is determined by using PCR amplification, clone and primer-walking sequencing methods. The genome is 16836 bp in size, containing 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. The mtDNA genome of Siamensis Crocodile is similar to most vertebrates in gene component, order, orientation, tRNA structure, low percentage of guanine and high percentage of thymine. The nonstandard stop codes (T) in two protein genes (Cox III and Cyt b) are more than those of most vertebrates. Transfer RNA genes range in length from 61 to 76 nucleotides, and their planar structure present characteristic clover leaf, except for tRNA-Ser (AGY) because of lacking the “DHU” arm.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

References

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

    PubMed  Article  CAS  Google Scholar 

  2. Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, Hay JM, Mindell DP (2003) Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol Phylogenet Evol 29(2):289–297

    PubMed  Article  CAS  Google Scholar 

  3. Boore JL (2004) Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. BMC Genomics 5(1):67

    PubMed  Article  CAS  Google Scholar 

  4. Garesse R, Carrodeguas JA, Santiago J, Perez ML, Marco R, Vallejo CG (1997) Artemia mitochondrial genome: molecular biology and evolutive considerations. Comp Biochem Physiol B Biochem Mol Biol 117(3):357–366

    PubMed  Article  CAS  Google Scholar 

  5. Zardoya R, Meyer A (1998) Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA 95(24):14226–14231

    PubMed  Article  CAS  Google Scholar 

  6. Janke A, Erpenbeck D, Nilsson M, Arnason U (2001) The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny. Proc Biol Sci 268(1467):623–631

    PubMed  Article  CAS  Google Scholar 

  7. Wu XB, Wang YQ, Zhou KY, Zhu WQ, Nie JS, Wang CL (2003) The complete mitochondrial genome sequence of Chinese alligator and the phylogeny of crocodiles. Chin Sci Bull 48(18):1954–1958

    Google Scholar 

  8. Mook CC (1921) Note on the postcranial skeleton in the Crocodilia. Bull Am Mus Nat Hist XLIV:67–100

    Google Scholar 

  9. Temsiripong Y, P. Ratanakorn (2001) A review for reintroduction program of Siamese crocodile in Thailand. Proceedings of the Regional Working Meeting of the Crocodile Specialist Group, Guangzhou, China, IUCN-The World Conservation Union, Gland, Switzerland and Cambridge UK. Temsiripong, Y. Re-introduction of the Siamese crocodile. CSG Newsletter; 20(1), pp 10–13

  10. Janke A, Arnason U (1997) The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). Mol Biol Evol 14:1266–1272

    PubMed  CAS  Google Scholar 

  11. Janke A, Gullberg A, Hughes S, Aggarwal RK, Arnason U (2005) Mitogenomic analyses place the gharial (Gavialis gangeticus) on the crocodile tree and provide pre-K/T divergence times for most crocodilians. J Mol Evol 61(5):620–626

    PubMed  Article  CAS  Google Scholar 

  12. Ji XF, Wu XB, Li Y, Yan P, Amato G (2006) The mitochondrial genome of Crocodylus niloticus with implications for phylogenetic relationships among crocodilian species. Acta Zool Sinica 52(4):810–818

    CAS  Google Scholar 

  13. Li Y, Wu XB, Ji XF, Yan P, Amato G (2006) The complete mitochondrial genome of the Salt-water Crocodile (Crocodylus porosus) and phylogeny of crocodiles. Acta Genet Sinica 2

  14. Arnason U, Gullberg A, Widegren B (1991) The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. J Mol Evol 33(6):556–568

    PubMed  Article  CAS  Google Scholar 

  15. 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(24):4876–4882

    PubMed  Article  CAS  Google Scholar 

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

    PubMed  CAS  Article  Google Scholar 

  17. Asakawa S, Kumazawa Y, Araki T, Himeno H, Miura K, Watanabe K (1991) Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J Mol Evol 32:511–520

    PubMed  Article  CAS  Google Scholar 

  18. Ray DA, Densmore L (2002) The Crocodilian mitochondrial control region: general structure, conserved sequences and evolutionary implications. J Exp Zool 294(4):334–345

    PubMed  Article  CAS  Google Scholar 

  19. Clayton DA (1982) Replication of animal mitochondrial DNA. Cell 28(4):693–705

    PubMed  Article  CAS  Google Scholar 

  20. Clayton DA (1984) Transcription of the mammalian mitochondrial genome. Annu Rev Biochem 53:573–594

    PubMed  Article  CAS  Google Scholar 

  21. Wong TW, Clayton DA (1985) In vitro replication of human mitochondrial DNA: accurate initiation at the origin of light-strand synthesis. Cell 42(3):951–958

    PubMed  Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by National Natural Science Foundation of China (NSFC, No. 30470244), the Foundations for Excellent Youth in Anhui Province (04043409) and Key Laboratory of Biotic Environment and Ecological safety in Anhui Province.

Author information

Affiliations

  1. College of Life Sciences, Anhui Key Laboratory of Conservation and Exploration for Important Biological Resource, Anhui Normal University, Wuhu, 241000, China

    Xuefeng Ji, Xiaobing Wu & Peng Yan

  2. Molecular Systematics Laboratory, American Museum of Natural History, New York, NY, USA

    George Amato

Authors
  1. Xuefeng Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiaobing Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peng Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. George Amato
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiaobing Wu.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ji, X., Wu, X., Yan, P. et al. Complete sequence and gene organization of the mitochondrial genome of Siamensis Crocodile (Crocodylus siamensis). Mol Biol Rep 35, 133–138 (2008). https://doi.org/10.1007/s11033-007-9062-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-007-9062-x

Keywords

  • Crocodylus siamensis
  • Genome
  • Mitochondrial
  • Structure