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The complete mitochondrial genome analysis of the tiger (Panthera tigris)

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An Erratum to this article was published on 01 August 2012

Abstract

The complete mitochondrial genomes of five tiger samples from three subspecies (P. t. sumatrae, P. t. altica, and P. t. tigris) were successfully obtained by using 26 specifically designed Panthera-specific primer sets. The genome organization and gene arrangement of the five tiger samples were similar to each other; however polymorphic tandem repeat sequences were observed in the control region (CR). This led to a difference in the genome lengths obtained from these five samples with an average size of 16,994 bp for the five tiger mitochondrial genomes. The nucleotide base composition was on average as follows: A, 31.8%; T, 27.0%; C, 26.6%; G, 14.6% and exhibited compositional asymmetry. Most of tiger mitochondrial genome characteristics are similar to those of other common vertebrate species; however, some distinctive features were observed in the CR. First, the repetitive sequence 2 (RS 2) contained two repeat units of 80 bp and the first 15 bp of what would be the third repeat motif. The repetitive sequence 3 (RS 3) contained 47–50 repeat motifs of a shorter 8 bp (ACGTAYAC)n. Second, length heteroplasmy polycystosine (poly-C) stretches was observed at the end of the HV I locus in all tiger samples.

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References

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

    Article  PubMed  CAS  Google Scholar 

  2. Wolstenholme DR (1992) Genetic novelties in mitochondrial genomes of multicellular animals. Curr Opin Genet Dev 2(6):918–925

    Article  PubMed  CAS  Google Scholar 

  3. Linacre A (2006) Application of mitochondrial DNA technologies in wildlife investigations—species identification. Forensic Sci Rev 18(1):1–8

    Google Scholar 

  4. Harrison RG (1989) Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol Evol 4:6–11

    Article  PubMed  CAS  Google Scholar 

  5. Pereira SL (2000) Mitochondrial genome organization and vertebrate phylogenetics. Genet Mol Biol 23:745–752

    Article  CAS  Google Scholar 

  6. Taberlet P, Bouvet J (1994) Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. Proc Biol Sci 255(1344):195–200. doi:10.1098/rspb.1994.0028

    Article  PubMed  CAS  Google Scholar 

  7. Yu L, Li Y-W, Ryder O, Zhang Y-P (2007) Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evol Biol 7(1):198

    Article  PubMed  Google Scholar 

  8. Schmitz Jr, Ohme M, Zischler H (2000) The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of Scandentia to other Eutherian orders. Mol Biol Evol 17(9):1334–1343

    Article  PubMed  CAS  Google Scholar 

  9. Cunha RL, Grande C, Zardoya R (2009) Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol Biol 9:210. doi:10.1186/1471-2148-9-210

    Article  PubMed  Google Scholar 

  10. Arnason U, Johnsson E (1992) The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina. J Mol Evol 34:493–505

    Article  PubMed  CAS  Google Scholar 

  11. Xu X, Arnason U (1996) The mitochondrial DNA molecule of Sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan. J Mol Evol 43(5):431–437

    Article  PubMed  CAS  Google Scholar 

  12. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290(5806):457–465

    Article  PubMed  CAS  Google Scholar 

  13. Lopez JV, Cevario S, O’Brien SJ (1996) Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33(2):229–246. doi:10.1006/geno.1996.0188

    Article  PubMed  CAS  Google Scholar 

  14. Kim JH, Antunes A, Luo SJ, Menninger J, Nash WG, O’Brien SJ, Johnson WE (2006) Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species. Gene 366(2):292–302. doi:10.1016/j.gene.2005.08.023

    Article  PubMed  CAS  Google Scholar 

  15. 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. doi:10.1093/molbev/msm092

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  17. Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13(5):660–665

    Article  PubMed  CAS  Google Scholar 

  18. Burger PA, Steinborn R, Walzer C, Petit T, Mueller M, Schwarzenberger F (2004) Analysis of the mitochondrial genome of cheetahs (Acinonyx jubatus) with neurodegenerative disease. Gene 338(1):111–119. doi:10.1016/J.Gene.2004.05.020

    Article  PubMed  CAS  Google Scholar 

  19. Wu XB, Zheng T, Jiang ZG, Wei L (2007) The mitochondrial genome structure of the clouded leopard (Neofelis nebulosa). Genome 50(2):252–257. doi:10.1139/G06-143

    Article  PubMed  CAS  Google Scholar 

  20. Wei L, Wu XB, Jiang ZG (2009) The complete mitochondrial genome structure of snow leopard Panthera uncia. Mol Biol Rep 36(5):871–878. doi:10.1007/S11033-008-9257-9

    Article  PubMed  CAS  Google Scholar 

  21. Kim KS, Lee SE, Jeong HW, Ha JH (1998) The complete nucleotide sequence of the domestic dog (Canis familiaris) mitochondrial genome. Mol Phylogenet Evol 10(2):210–220. doi:10.1006/mpev.1998.0513

    Article  PubMed  CAS  Google Scholar 

  22. Ursing BM, Arnason U (1998) The complete mitochondrial DNA sequence of the pig (Sus scrofa). J Mol Evol 47(3):302–306

    Article  PubMed  CAS  Google Scholar 

  23. Gissi C, Gullberg A, Arnason U (1998) The complete mitochondrial DNA sequence of the rabbit, Oryctolagus cuniculus. Genomics 50(2):161–169. doi:10.1006/geno.1998.5282

    Article  PubMed  CAS  Google Scholar 

  24. Saccone C, De Giorgi C, Gissi C, Pesole G, Reyes A (1999) Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238(1):195–209

    Article  PubMed  CAS  Google Scholar 

  25. Xu X, Gullberg A, Arnason U (1996) The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs. J Mol Evol 43(5):438–446

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  27. 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 

  28. Kumazawa Y, Nishida M (1993) Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol 37(4):380–398

    Article  PubMed  CAS  Google Scholar 

  29. Hoelzel AR, Lopez JV, Dover GA, O’Brien SJ (1994) Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J Mol Evol 39(2):191–199

    PubMed  CAS  Google Scholar 

  30. Freeman AR, MacHugh DE, McKeown S, Walzer C, McConnell DJ, Bradley DG (2001) Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Acinonyx jubatus). Heredity 86(Pt 3):355–362. doi:10.1046/j.1365-2540.2001.00840.x

    Article  PubMed  CAS  Google Scholar 

  31. Mignotte F, Gueride M, Champagne AM, Mounolou JC (1990) Direct repeats in the non-coding region of rabbit mitochondrial DNA. Involvement in the generation of intra- and inter-individual heterogeneity. Eur J Biochem 194(2):561–571

    Article  PubMed  CAS  Google Scholar 

  32. Wilkinson GS, Chapman AM (1991) Length and sequence variation in evening bat D-loop mtDNA. Genetics 128(3):607–617

    PubMed  CAS  Google Scholar 

  33. Hoelzel AR, Hancock JM, Dover GA (1993) Generation of VNTRs and heteroplasmy by sequence turnover in the mitochondrial control region of two elephant seal species. J Mol Evol 37(2):190–197

    Article  PubMed  CAS  Google Scholar 

  34. Ghivizzani SC, Mackay SL, Madsen CS, Laipis PJ, Hauswirth WW (1993) Transcribed heteroplasmic repeated sequences in the porcine mitochondrial DNA D-loop region. J Mol Evol 37(1):36–37

    Article  PubMed  CAS  Google Scholar 

  35. Freeman AR, Machugh DE, McKeown S, Walzer C, McConnell DJ, Bradley DG (2001) Sequence variation in the mitochondrial DNA control region of wild African cheetahs (Acinonyx jubatus). Heredity 86(3):355–362

    Article  PubMed  CAS  Google Scholar 

  36. Holland MM, Parsons TJ (1999) Mitochondrial DNA sequence analysis—validation and use for forensic casework. Forensic Sci Rev 11:21–50

    Google Scholar 

  37. Seo SB, Jang BS, Zhang A, Yi JA, Kim HY, Yoo SH, Lee YS, Lee SD (2010) Alterations of length heteroplasmy in mitochondrial DNA under various amplification conditions. J Forensic Sci 55(3):719–722. doi:10.1111/J.1556-4029.2010.01321.X

    Article  PubMed  CAS  Google Scholar 

  38. Bendall KE, Sykes BC (1995) Length heteroplasmy in the first hypervariable segment of the human mtDNA control region. Am J Hum Genet 57(2):248–256

    PubMed  CAS  Google Scholar 

  39. Mooers Aÿ, Holmes EC (2000) The evolution of base composition and phylogenetic inference. Trends Ecol Evol 15(9):365–369

    Article  PubMed  Google Scholar 

  40. Clayton DA (1982) Replication of animal mitochondrial DNA. Cell 28(4):693–705. doi:10.1016/0092-8674(82)90049-6

    Article  PubMed  CAS  Google Scholar 

  41. Parsons P, Simpson MV (1973) Deoxyribonucleic acid biosynthesis in mitochondria. Studies on the incorporation of labeled precursors into mitochondrial deoxyribonucleic acid. J Biol Chem 248(6):1912–1919

    PubMed  CAS  Google Scholar 

  42. Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41(3):353–358. doi:10.1007/bf00186547

    Article  PubMed  CAS  Google Scholar 

  43. Reyes A, Gissi C, Pesole G, Saccone C (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol Biol Evol 15(8):957–966

    Article  PubMed  CAS  Google Scholar 

  44. Tanaka M, Ozawa T (1994) Strand asymmetry in human mitochondrial DNA mutations. Genomics 22(2):327–335

    Article  PubMed  CAS  Google Scholar 

  45. Brown GG, Simpson MV (1982) Novel features of animal mtDNA evolution as shown by sequences of two rat cytochrome oxidase subunit II genes. Proc Natl Acad Sci USA 79(10):3246–3250

    Article  PubMed  CAS  Google Scholar 

  46. Bulmer M (1987) Coevolution of codon usage and transfer RNA abundance. Nature 325(6106):728–730. doi:10.1038/325728a0

    Article  PubMed  CAS  Google Scholar 

  47. Haruyama N, Mochizuki A, Sato Y, Naka H, Nomura M (2011) Complete mitochondrial genomes of two green lacewings, Chrysoperla nipponensis (Okamoto, 1914) and Apochrysa matsumurae Okamoto, 1912 (Neuroptera: Chrysopidae). Mol Biol Rep 38(5):3367–3373. doi:10.1007/s11033-010-0444-0

    Article  PubMed  CAS  Google Scholar 

  48. Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10(22):7055–7074

    Article  PubMed  CAS  Google Scholar 

  49. Robinson M, Lilley R, Little S, Emtage JS, Yarranton G, Stephens P, Millican A, Eaton M, Humphreys G (1984) Codon usage can affect efficiency of translation of genes in Escherichia coli. Nucleic Acids Res 12(17):6663–6671

    Article  PubMed  CAS  Google Scholar 

  50. Sharp PM, Stenico M, Peden JF, Lloyd AT (1993) Codon usage: mutational bias, translational selection, or both? Biochem Soc Trans 21(4):835–841

    PubMed  CAS  Google Scholar 

  51. Xia X (1996) Maximizing transcription efficiency causes codon usage bias. Genetics 144(3):1309–1320

    PubMed  CAS  Google Scholar 

  52. Zama M (1990) Codon usage and secondary structure of mRNA. Nucleic Acids Symp Ser 22:93–94

    PubMed  CAS  Google Scholar 

  53. Oresic M, Shalloway D (1998) Specific correlations between relative synonymous codon usage and protein secondary structure. J Mol Biol 281(1):31–48

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This research was supported by the South Australia Ministry of Justice and Royal Thai Government. The authors would also like to thank the Isle of Wight Zoo and National Museums of Scotland for the contribution of species samples.

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  1. School of Biological Sciences, Flinders University, Adelaide, 5001, Australia

    Thitika Kitpipit & Adrian Linacre

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  1. Thitika Kitpipit
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  2. Adrian Linacre
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Correspondence to Adrian Linacre.

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Kitpipit, T., Linacre, A. The complete mitochondrial genome analysis of the tiger (Panthera tigris). Mol Biol Rep 39, 5745–5754 (2012). https://doi.org/10.1007/s11033-011-1384-z

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