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Molecular Biology Reports

, Volume 38, Issue 1, pp 593–599 | Cite as

The complete mitochondrial genome and phylogenetic analysis of the Debao pony (Equus caballus)

  • Qinyang Jiang
  • Yingming Wei
  • Yanna Huang
  • Hesheng Jiang
  • Yafen Guo
  • Ganqiu Lan
  • D. Joshua Liao
Article

Abstract

The Debao pony (Equus caballus) is the most important local variety of domestic horses, and is strictly protected by the Chinese government. Their average adult withers height is 94.42 ± 3.76 cm for males and 98.35 ± 4.55 cm for females, respectively. In the present study, the complete sequence of the Debao pony mitochondrial genome was determined (GenBank Accession No. EU939445), and was found to be similar to other equine mitochondrial genomes. However, there were 85 nucleotide substitutions in the 13 protein-coding genes; the percentage of substitution was 0.8 ± 0.1. Polymorphisms of mtDNA control regions were analyzed with restriction fragment length polymorphism (RFLP), and 19 haplotypes were found, with a genetic diversity of 0.77. Neighbor-Joining (NJ) and Minimum Evolution (ME) trees based on complete control regions of mtDNA were constructed with the Maximum Composite Likelihood (MCL) method. The analysis indicated that the origins of the Debao pony were scattered in the various branches of the phylogenetic tree. The results from the present study suggest that the Debao pony is derived from multi-matrilineal origins of the species.

Keywords

Debao pony Mitochondrial genome Haplotype Phylogenetic tree 

Notes

Acknowledgments

We thank Fred Bogott, M.D. and Ph.D., for his excellent English editing of the manuscript. We also thank the staffs of the Fishery, Husbandry and Veterinary Bureau of Debao Country of Guangxi Zhuang autonomous region, P.R. China, for their kind assistance in collecting blood samples of the Debao ponies. This study was supported by the Science Foundation of Guangxi Zhuang autonomous region (0640014 and 0992028-9).

References

  1. 1.
    Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780CrossRefPubMedGoogle Scholar
  2. 2.
    Peng R, Zeng B, Meng X, Yue B, Zhang Z, Zou F (2007) The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Gene 397:76–83CrossRefPubMedGoogle Scholar
  3. 3.
    Ki J-S, Hwang D-S, Park T-J, Han S-H, Lee J-S (2010) A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae). Mol Biol Rep 37:1943–1955CrossRefPubMedGoogle Scholar
  4. 4.
    Ji X, Wu X, Yan P, Amato G (2008) Complete sequence and gene organization of the mitochondrial genome of Siamensis Crocodile (Crocodylus siamensis). Mol Biol Rep 35(2):133–138CrossRefPubMedGoogle Scholar
  5. 5.
    Jiang F, Miao Y, Liang W, Ye H, Liu H, Liu B (2009) The complete mitochondrial genomes of the whistling duck (Dendrocygna javanica) and black swan (Cygnus atratus): dating evolutionary divergence in Galloanserae. Mol Biol Rep. doi: 10.1007/s11033-009-9868-9
  6. 6.
    Vilá C, Leonard JA, Gotherstom A, Marklund S, Sandberg K, Lindén K, Wayne RK, Ellegren H (2001) Wide spread origin of domestic horse lineages. Science 291:474–477CrossRefPubMedGoogle Scholar
  7. 7.
    Kavar T, Brem G, Habe F, Sokner J, Dov P (2002) History of Lipizzan horse maternal lines as revealed by mtDNA analysis. Genet Sel Evol 34:635–648CrossRefPubMedGoogle Scholar
  8. 8.
    Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C, Weber J, Olek K (2002) Mitochondrial DNA and the origins of the domestic horse. Proc Natl Acad Sci USA 99:10905–10910CrossRefPubMedGoogle Scholar
  9. 9.
    Yang YH, Kim KI, Cothran EG, Flannery AR (2002) Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism. Biochem Genet 40:5–6Google Scholar
  10. 10.
    Luis C, Bastos-Silveira C, Gus Cothran E, Do Mar Oom M (2006) Iberian origins of new world horse breeds. J Hered 97:107–113CrossRefPubMedGoogle Scholar
  11. 11.
    Iwaňczyk E, Juras R, Cholewiňski G, Gus Cothran E (2006) Genetic structure and phylogenetic relationships of the Polish heavy horse. J Appl Genet 47:353–359PubMedGoogle Scholar
  12. 12.
    Harrison SP, Turrion-Gomez JL (2006) Mitochondrial DNA: an important female contribution to thoroughbred race horse performance. Mitochondrion 6:53–66PubMedGoogle Scholar
  13. 13.
    Kakoi H, Tozaki T, Gawahara H (2007) Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations. Biochem Genet 45:150–163CrossRefGoogle Scholar
  14. 14.
    Avdi M, Banos G (2008) Genetic diversity and inbreeding in the Greek Skyros horse. Livest Sci 14:362–365Google Scholar
  15. 15.
    Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Press, Cold Spring Harbor, New YorkGoogle Scholar
  16. 16.
    Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030–11035CrossRefPubMedGoogle Scholar
  17. 17.
    Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedGoogle Scholar
  18. 18.
    Tamura K, Dudley J, Nei M, Kumar S (2007) Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  19. 19.
    Saitou MN, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  20. 20.
    Rzhetsky MA, Nei M (1992) A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 9:945–967Google Scholar
  21. 21.
    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  22. 22.
    Boore JL (2001) Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii. Mol Biol Evol 18:1413–1416PubMedGoogle Scholar
  23. 23.
    Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426PubMedGoogle Scholar
  24. 24.
    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 32:511–520CrossRefPubMedGoogle Scholar
  25. 25.
    Haring E, Kruckenhauser L, Gamauf A, Riesing MJ, Pinsker W (2001) The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors. Mol Biol Evol 18:1892–1904PubMedGoogle Scholar
  26. 26.
    Yang R, Wu X, Yan P, Su X, Yang B (2009) Complete mitochondrial genome of Otis tarda (Gruiformes: Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences. Mol Biol Rep. doi: 10.1007/s11033-009-9878-7
  27. 27.
    Lin C-S, Sun Y-L, Liu C-Y, Yang P-C, Chang L-C, Cheng I-C, Mao SJT, Huang M-C (1999) Complete nucleotide sequence of pig (Sus scrofa) mitochondrial genome and dating evolutionary divergence within Artiodactyla. Gene 236:107–114CrossRefPubMedGoogle Scholar
  28. 28.
    Wei L, Wu X, Jiang Z (2009) The complete mitochondrial genome structure of snow leopard Panthera uncia. Mol Biol Rep 36(5):871–878. Epub 23 Apr 2008. PubMed PMID: 18431688Google Scholar
  29. 29.
    Xu X, Arnason U (1994) The complete mitochondrial DNA sequence of the horse (Equus caballus): extensive heteroplasmy of the control region. Gene 148(2):357–362CrossRefPubMedGoogle Scholar
  30. 30.
    Lister AM, Kadwell M, Kaagan LM, Jordan WC, Richards MB, Stanley HF (1998) Ancient and modern DNA in study of horse domestication. Anc Biomol 2:267–280Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Qinyang Jiang
    • 1
  • Yingming Wei
    • 1
  • Yanna Huang
    • 2
  • Hesheng Jiang
    • 1
    • 3
  • Yafen Guo
    • 1
  • Ganqiu Lan
    • 1
  • D. Joshua Liao
    • 4
  1. 1.College of Animal Science and TechnologyGuangxi UniversityNanningPeople’s Republic of China
  2. 2.Institute of Feed ScienceZhejiang UniversityHangzhouPeople’s Republic of China
  3. 3.Guangxi Academy of SciencesNanningPeople’s Republic of China
  4. 4.Hormel InstituteUniversity of MinnesotaAustinUSA

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