Molecular Biology Reports

, Volume 35, Issue 2, pp 133–138

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

Original Paper

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.

Keywords

Crocodylus siamensis Genome Mitochondrial Structure 

References

  1. 1.
    Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27(8):1767–1780PubMedCrossRefGoogle Scholar
  2. 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):289–297PubMedCrossRefGoogle Scholar
  3. 3.
    Boore JL (2004) Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. BMC Genomics 5(1):67PubMedCrossRefGoogle Scholar
  4. 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):357–366PubMedCrossRefGoogle Scholar
  5. 5.
    Zardoya R, Meyer A (1998) Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA 95(24):14226–14231PubMedCrossRefGoogle Scholar
  6. 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):623–631PubMedCrossRefGoogle Scholar
  7. 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):1954–1958Google Scholar
  8. 8.
    Mook CC (1921) Note on the postcranial skeleton in the Crocodilia. Bull Am Mus Nat Hist XLIV:67–100Google Scholar
  9. 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 10–13Google Scholar
  10. 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 14:1266–1272PubMedGoogle Scholar
  11. 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):620–626PubMedCrossRefGoogle Scholar
  12. 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):810–818Google Scholar
  13. 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 2Google Scholar
  14. 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):556–568PubMedCrossRefGoogle Scholar
  15. 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):4876–4882PubMedCrossRefGoogle Scholar
  16. 16.
    Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173–216PubMedCrossRefGoogle Scholar
  17. 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 32:511–520PubMedCrossRefGoogle Scholar
  18. 18.
    Ray DA, Densmore L (2002) The Crocodilian mitochondrial control region: general structure, conserved sequences and evolutionary implications. J Exp Zool 294(4):334–345PubMedCrossRefGoogle Scholar
  19. 19.
    Clayton DA (1982) Replication of animal mitochondrial DNA. Cell 28(4):693–705PubMedCrossRefGoogle Scholar
  20. 20.
    Clayton DA (1984) Transcription of the mammalian mitochondrial genome. Annu Rev Biochem 53:573–594PubMedCrossRefGoogle Scholar
  21. 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):951–958PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Xuefeng Ji
    • 1
  • Xiaobing Wu
    • 1
  • Peng Yan
    • 1
  • George Amato
    • 2
  1. 1.College of Life Sciences, Anhui Key Laboratory of Conservation and Exploration for Important Biological ResourceAnhui Normal UniversityWuhuChina
  2. 2.Molecular Systematics LaboratoryAmerican Museum of Natural HistoryNew YorkUSA

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