156
Views
22
CrossRef citations to date
0
Altmetric
Original

The complete mitochondrial genome of the Korean soft-shelled turtle Pelodiscus sinensis (Testudines, Trionychidae)

Full Length Research Paper

, , , , &
Pages 471-483 | Received 19 Apr 2005, Published online: 11 Jul 2009

References

  • Anderson S, Bankier AT, Barrell BG, de Bruijin MHL, Coulson AR, Drouin J, Eperon IC, Pengrlich CDP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG. Sequence and organization of the human mitochondrial genome. Nature 1981; 290: 457–465
  • Attardi G. Animal mitochondrial DNA: An extreme example of genetic economy. Int Rev Cytol 1985; 93: 93–145
  • Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA. Sequence and gene organization of mouse mitochondrial DNA. Cell 1981; 26: 167–180
  • Broughton RE, Milam JE, Roe BA. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 2001; 11: 1958–1967
  • Cao Y, Sorenson MD, Kumazawa Y, Mindell DP, Hasegawa M. Phylogenetic position of turtles among amniotes: Evidence from mitochondrial and nuclear genes. Gene 2000; 259: 139–148
  • Doda JN, Wright CT, Clayton DA. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA 1981; 78: 6116–6120
  • Dutton PH, Davis SK, Guerra T, Owens D. Molecular phylogeny for marine turtles bases on sequences of the ND4-leucine tRNA and control regions of mitochondrial DNA. Mol Phylogenet Evol 1996; 5: 511–521
  • Encalada SE, Lahanas PN, Bjorndal KA, Bolten AB, Miyamoto MM, Bowen BW. Phylogeography and population structure of the Atlantic and Mediterranean green turtle Chelonia mydas: A mitochondrial DNA control region sequence assessment. Mol Ecol 1996; 5: 473–483
  • Engstrom TN, Shaffer HB, McCord WP. Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae). Syst Biol 2004; 53: 693–710
  • Farajallah A, Suryobroto B, Setyadji R, Perwitasari-Farajallah D, Osamu T. 2006. The complete nucleotide sequence of Malayan soft-shelled turtle (Dogania subplana) mitochondrial genome, Unpublished.
  • Gutell RR, Gray MW, Schnare MN. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res 1993; 21: 3055–3074
  • Hebert PD, Stoeckle MY, Zemlak TS, Francis CM. Identification of birds through DNA barcodes. PLoS Biol 2004; 2: e312
  • Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001; 17: 754–755
  • Iwabe N, Hara Y, Kumazawa Y, Shibamoto K, Saito Y, Miyata T, Katoh K. Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins. Mol Biol Evol 2005; 22: 810–813
  • Johns GC, Avise JC. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol 1998; 15: 1481–1490
  • Jung S-O, Lee Y-M, Park T-J, Park HG, Hagiwara A, Leung K-MY, Dahms H-U, Lee W, Lee J-S. The complete mitochondrial genome of the intertidal copepod Tigriopus sp. (Copepoda, Harpactidae) from Korea and phylogenetic considerations. J Exp Mar Biol Ecol 2006; 325
  • Kartavtsev YP, Lee J-S. Analysis of nucleotide diversity at genes Cyt-b and Co-1 on population, species, and genera levels. Applicability of DNA and allozyme data in genetics of speciation. Russian J Genet 2006; 42: 341–362
  • Kartavtsev YP, Lee Y-M, Jung S-O, Byeon H-K, Lee J-S. The complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cyt b gene. Gene 2006, (in revision)
  • Kim I-C, Lee J-S. The complete mitochondrial genome of the rockfish Sebastes schlegeli (Scorpaeniformes Scorpaenidae). Mol Cells 2004; 17: 322–328
  • Kim Y-J, Kweon H-S, Kim I-C, Lee Y-M, Kim JM, Lee J-S. The complete mitochondrial genome of the floating goby, Gymnogobius petschiliensis (Perciformes, Gobiidae). Mol Cells 2004a; 17: 446–453
  • Kim I-C, Kweon H-S, Kim YJ, Kim C-B, Gye MC, Lee W-O, Lee Y-S, Lee J-S. The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes Gobiidae) and phylogenetic considerations. Gene 2004b; 336: 147–153
  • Kim I-C, Jung S-O, Lee Y-M, Lee CJ, Park J-K, Lee J-S. The complete mitochondrial genome of the rayfish Raja porosa (Chondrichthyes Rajidae). DNA Seq 2005; 16: 187–194
  • Kinouchi M, Kanaya S, Ikemura T, KudoY. Detection of tRNA based on the cloverleaf secondary structure. Genome Informat 2000; 11: 301–302
  • Kumazawa Y, Nishida M. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol 1993; 37: 380–398
  • Kumazawa Y, Nishida M. Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Mol Biol Evol 1995; 12: 759–772
  • Kumazawa Y, Nishida M. Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: Statistical evidence for archosaurian affinity of turtles. Mol Biol Evol 1999; 16: 784–792
  • Lahanas PN, Miyamoto MM, Bjorndal KA, Bolten AB. Molecular evolution and population genetics of Greater Caribbean green turtles (Chelonina mydas) as inferred from mitochondrial DNA control region sequences. Genetica 1994; 94: 57–66
  • Lamb T, Lydeard C. A molecular phylogeny of the gopher tortoises, with comments on familial relationships within the Tesudinoidea. Mol Phylogenet Evol 1994; 3: 283–291
  • Lee J-S. The internally self-fertilizing hermaphroditic teleost Rivulus marmoratus (Cyprinodontiformes Rivulidae) β-actin gene: amplification and sequence analysis with conserved primers. Mar Biotechnol 2000; 2: 161–166
  • Lee J-S, Miya M, Lee Y-S, Kim CG, Park E-H, Aoki Y, Nishida M. The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes Rivulidae) and the first finding of duplication of control region in fish. Gene 2001; 280: 1–7
  • Marshall HD, Baker AJ. Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and the greenfinch (Carduelis chloris). Mol Biol Evol 1997; 14: 173–184
  • Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst Biol 1999; 48: 138–152
  • Miya M, Nishida M. Organization of the mitochondrial genome of a deep-dea fish, Gonostoma gracile (Teleostei: Stomiiformers): First example of transfer RNA gene rearragenements in bony fishes. Mar Biotechnol 1999; 1: 416–426
  • Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M. Major patterns of higher teleostean phylogePengs: A new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 2003; 26: 121–138
  • Naylor GJ, Collins TM, Brown WM. Hydrophobicity and phylogeny. Nature 1996; 373: 565–566
  • Nei M, Kumar S. Molecular Evolution and Phylogenetics. Oxford University Press, New York 2000; 333
  • Page RDM. TREEVIEW: An application to display phylogenetic trees on personal computers. Comp Appl Biosci 1996; 12: 357–358
  • Peng Q, Pu Y, Peng L. Complete mitochondrial DNA sequence of Chinese softshell turtle (Pelodiscus sinensis). Chin J Biochem Mol Biol 2005; 21, in press
  • Posada D, Crandall KA. MODELTEST: Testing the model of DNA substitution. Bioinformatics 1998; 14: 817–818
  • Quinn TW, Mindell DP. Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara. Mol Phylogenet Evol 1996; 5: 344–351
  • Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, Hay JM, Mindell DP. Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Mol Phylogenet Evol 2003; 29: 289–297
  • Seddon JM, Baverstock PR, Georges A. The rate of mitochondrial 12S rRNA gene evolution is similar in freshwater turtles and marsupials. J Mol Evol 1998; 46: 460–464
  • Seutin G, Lang BF, Mindell DP, Morais R. Evolution of the WANCY region in amniote mitochondrial DNA. Mol Biol Evol 1994; 11: 329–340
  • Spinks PQ, Shaffer HB, Iverson JB, McCord WP. Phylogenetic hypotheses for the turtle family Geoemydidae. Mol Phylogenet Evol 2004; 32: 164–182
  • Starkey DE, Shaffer HB, Burke RL, Forstner MR, Iverson JB, Janzen FJ, Rhodin AG, Ultsch GR. Molecular systematics, phylogeography, and the effects of Pleistocene glaciation in the painted turtle (Chrysemys picta) complex. Evolution 2003; 57: 119–128
  • Swofford DL. PAUP: Phylogenetic Analysis Using Parsimony, Version 4.10. Sinauer Associates, Sunderland, MA 2002
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1977. The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882.
  • Ueda T, Yotsumoto Y, Ikeda K, Watanabe K. The T-loop region of animal mitochondrial tRNASer(AGY) is a main recognition site for homologous seryl-tRNA synthetase. Nucleic Acids Res 1992; 20: 2217–2222
  • Van der Kuyl AC, Ballasina DLP, Dekker JT, Maas J, Willemsen RE, Goudsmit J. Phylogenetic relationships among the species of the genus Testudo (Testudinidae) inferred from mitochondrial 12S rRNA gene sequences. Mol Phylogenet Evol 2002; 22: 174–183
  • Walberg MW, Clayton DA. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res 1981; 9: 5411–5421
  • Weisrock DW, Janzen FJ. Comparative molecular phylogeography of North American softshell turtles (Apalone): Implications for regional and wide-scale historical evolutionary forces. Mol Phylogenet Evol 2000; 14: 152–164
  • Zardoya R, Meyer A. Cloning and characterization of a microsatellite in the mitochondrial control region of the African side-necked turtle, Pelomedusa subrufa. Gene 1998; 216: 149–153
  • Zardoya R, Meyer A. Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA 1998; 95: 14226–14231

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.