Abstract
In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.
Similar content being viewed by others
References
Tan B (1987) Status and problems of captive tigers in China. In: Tilson R, Seal U (eds) Tigers of the world: the biology biopolitics management and conservation of an endangered species. Noyes Publications, Park Ridge, pp 134–148
Tilson R, Defu H, Muntifering J, Nyhus PJ (2004) Dramatic decline of wild south China tigers Panthera tigris amoyensis: field survey of priority tiger reserves. Oryx 38(1):40–47
Yin YZ (2009) Studbook of the South China tiger. Chongqing Zoological Garden, China
Moore WS (1995) Inferring phylogenies from mtDNA variation: mitochondrial gene trees versus nuclear-gene trees. Evolution 49:718–726
Broughton RE, Reneau PC (2006) Spatial covariation of mutation and nonsynonymous substitution rates in vertebrate mitochondrial genomes. Mol Biol Evol 23:1516–1524
Luo S-J, Kim J-H, Johnson WE, Walt JVD, Martenson J, Yuhki N, Miquelle DG, Uphyrkina O, Goodrich JM, Quigley HB, Tilson R, Brady G, Martelli P, Subramaniam V, McDougal C, Hean S, Huang S-Q, Pan W-S, Karanth UK, Sunquist M, Smith JLD, O’Brien SJ (2004) Phylogeography and genetic ancestry of tigers (Panthera tigris). PLoS Biol 2(12):2275–2293
Luo S-J, Kim J-H, Johnson WE, Miquelle DG, Huang S-Q, Pan W-S, Smith JLD, O’Brien SJ (2006) Proceeding in phylogeography and genetic ancestry of tigers (Panthera tigris) in China and across their range. Zool Res (China) 27(4):441–448
Wei K, Zhang Z-H, Zhang W-P, Shen F-J, He G-X, Hou R, **e Z, Liu N-L, Yue B-S (2005) Sequence variation of mitochondrial DNA ND5 in captive South China tigers (Panthera tigris amoyensis). J Nat Hist 39(46):3979–3984
Driscoll CA, Yamaguchi N, Bar-Gal GK, Roca AL, Luo S, Macdonald DW, O’Brien SJ (2009) Mitochondrial phylogeography illuminates the origin of the extinct Caspian tiger and its relationship to the Amur Tiger. PLoS One 1:e4125
Kitpipit T, Linacre A, Tobe SS (2009) Tiger species identification based on molecular approach. Forensic Sci Int Genet Suppl Ser 2:310–312
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
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 25:4876–4882
Wu X, Zheng T, Jiang Z, Wei L (2007) The mitochondrial genome structure of the clouded leopard (Neofelis nebulosa). Genome 50:252–257
Wei L, Wu X, Jiang Z (2009) The complete mitochondrial genome structure of snow leopard Panthera uncial. Mol Biol Rep 36:871–878
Jae-Heup K, Eizirik E, O’Brien SJ, Johnson WE (2001) Structure and patterns of sequence variation in the mitochondrial DNA control region of the great cats. Mitochondrion 14:279–292
Leopez JV, Cevario S, O’Brien SJ (1996) Compelte nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33:229–246
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 338:111–119
Solignac M, Gebnermont J, Monnerot M, Mounolou JC (1987) Drosophila mitochondrial genetics: evolution of heteroplasmy through germ line cell divisions. Genetics 117:687–696
Casane D, Dennebouy N, de Rochambeau H, Mounolou JC, Monnerot M (1997) Nonneutral evolution of tandem repeats in the mitochondrial DNA control region of Lagomorphs. Mol Biol Evol 14:779–789
Brown JR, Beckenbach AT, Smith MJ (1993) Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus). Mol Biol Evol 10:326–341
Lopez JV, Culver M, Stephens JC, Johnson WE, O’Brien SJ (1997) Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Mol Biol Evol 14:277–286
Lopez JV, Yuhki N, Masuda R, Modi W, O’Brien SJ (1994) Numt, a recent transfer and Tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39(2):174–190
Johnson WE, Dratch PA, Martenson JS, O’Brien SJ (1996) Resolution of recent radiations within three evolutionary lineages of Felidae using mitochondrial restriction fragment length polymorphism variation. J Mamm Evol 3(2):97–120
Cracraft J, Felsenstein J, Vaughn J, Helm-Bychowski K (1998) Sorting out tigers (Panthera tigris): mitochondrial sequences, nuclear inserts, systematics, and conservation genetics. Anim Conserv 1:139–150
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
Zhang WP, Zhang ZH, Shen FJ, Hou R, Lv XP, Yue BS (2006) Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris). J Genet 85:107–116
Yao Y-G, Kong Q-P, Salas A, Bandelt H-J (2008) Pseudomitochondrial genome haunts disease studies. J Med Genet 45:769–772
Acknowledgments
This research was funded by National Natural Science Foundation of China (30870465), the Chengdu Giant Panda Foundation, and Longyan Science and Technology Bureau ([2009]48). We thank Guangxin He and Guanghan Li for conducting the sample collections, and Norian Caporale-Berkowitz for help with English editing.
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Zhang, W., Yue, B., Wang, X. et al. Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes. Mol Biol Rep 38, 4257–4264 (2011). https://doi.org/10.1007/s11033-010-0548-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11033-010-0548-6