Genes & Genomics

, Volume 32, Issue 4, pp 291–298 | Cite as

Comparison research and phylogenetic implications of mitochondrial control regions in four soft-shelled turtles of Trionychia (Reptilia, Testudinata)

Research Article
First Online:
Received:
Accepted:

Abstract

The mitochondrial control regions (CRs) and flanking sequences of Pelodiscus sinensis, Apalone ferox, Palea steindachneri and Carettochelys insculpta were obtained using Long-PCR with gene-specific primers. The CR lengths of the four species were 1843 bp, 1356 bp, 1725 bp, and 969 bp. The base composition percentages of A+T were 60.5%, 60.7%, 65.7%, 64.7%, respectively. Combined with CR sequences of other three soft-shelled turtles published in GenBank (Pelodiscus sinensis, Korea, AY962573; Dogania subplana, AF366350; Lissemys punctata, EF050073), we compared the CR structures and identified three functional domains (TAS, CD and CSB) in which conserved sequence blocks (TAS, CSB -F, CSB-1, CSB-2 and CSB-3) were also successfully identified according to their sequence similarities to those of other turtles. The variable numbers of tandem repeats (VNTRs 1) with 50–52 bp motif were identified at 5′-end of CR among the five soft-shelled turtles P. sinensis (China), P. sinensis (Korea), A. ferox, P. steindachneri, D. subplana. The copy number of the VNTRs varied from 5 to 15. VNTRs 2 with 2–11 bp motif were identified in the 3′- end of CR among all of the six soft-shelled turtles with variable number of motifs from 4 to 29. Moreover, VNTRs 3 with 6 bp motif were identified between CSB-1 and CSB-2 of CR both in P. sinensis (China) and P. sinensis (Korea), in which the number of motifs varied from 19 to 29. The types and distribution of VNTRs of the six soft-shelled turtles were also discussed. With Alligator mississippiensis as an outgroup, combined with the CR sequences (excluding VNTRs) of other five turtles which were published in GenBank, the molecular phylogenetic trees were constructed using PAUP 4.0b10 and MrBayes ver. 3.0. The results strongly supported the monophyly of Carretochelyidae and Carettochelyidae as sister group to an assemblage of Cryptodira. Our research suggested that the earliest phylogenetic tree splits into three separated basal branches; the Pelomedusidira (Pelomedusa subrufa), the Carettochelyidae (C. insculpta), and an assemblage of Cryptodira and the C. insculpta that might be a representation of distinctive suborder.

Key words

Trionychia Mitochondrial DNA Control region Variable numbers of tandem repeats Phylogenetic 
This is a preview of subscription content, log in to check access.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Anderson S, Bruijn HL, Coulson AR, Eperon IC, Sanger F and Young IG (1982) Complete sequence of bovine mitochondrial DNA: conserved features of the mammalian mitochondrial genome. Mol. Biol. 156: 683–717.CrossRefGoogle Scholar
  2. Barley AJ (2009) Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Mol. Phylogenet. Evol. 55: 1189–1194.CrossRefPubMedGoogle Scholar
  3. Brehm A, Harris DJ, Alves C, Jesus J, Thomarat F and Vicente L (2003) Structure and evolution of the mitochondrial DNA complete control region in the lizard Lacerta dugesii (Lacertidae Sauria). J. Mol. Evol. 56: 46–53.CrossRefPubMedGoogle Scholar
  4. Broughton RE and Dowling TE (1997) Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera. Mol. Biol. Evol. 14: 1187–1196.PubMedGoogle Scholar
  5. Buroker NE, Brown JR, Gilbert TA, O’Hara PJ, Beckenbach AT, Thomas WK and Smith MJ (1990) Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model. Genetics 124: 157–163.PubMedGoogle Scholar
  6. Delport W, Ferguson JWH and Bloomer P (2002) Characterization and evolution of the mitochondrial DNA control region in hornbills (Bucerotiformes). J. Mol. Evol. 54: 794–806.CrossRefPubMedGoogle Scholar
  7. Engstrom TN, Shaffer HB and Mccord WP (2004) Multiple DataSets, High Homoplasy, and the Phylogeny of Softshell Turtles (Testudines: Trionychidae). Syst. Biol. 53: 693–710.CrossRefPubMedGoogle Scholar
  8. Fang SG and Xu QH (2006) Variable number tandem repeats in the mitochondrial DNA Control region of the Chinese alligator, Alligator sinensis. Amphibia-Reptilia 27: 93–101.CrossRefGoogle Scholar
  9. Foran DR, Hixson JE and Brown WM (1988) Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and Dloop synthesis. Nucl. Acids Res. 16: 5841–5861.CrossRefPubMedGoogle Scholar
  10. Fritz U and Havas P (2007) Checklist of Chelonians of the World. Verteb. Zool. 57(2): 149–368.Google Scholar
  11. Fujita MK, Engstrom TN, Starkey DE and Shaffer HB (2004) Turtle phylogeny: Insights from a novel nuclear intron. Mol. Phylogenet. Evol. 31: 1031–1040.CrossRefPubMedGoogle Scholar
  12. Fu YY, Gu WW, Liu YZ, Peng JY and Chang H (2006) Genetic analysis of the polymorphism of mtDNA D-loop and microsatellite loci in Tibet mini-pigs. Acta Laboratorium Animalis Scientia Sinica 14: 318–321.Google Scholar
  13. Gaffney ES and Meylan PA (1988) A phylogeny of turtles. Pages 157–219 in the phylogeny and classification of tetrapods (M.J. Benton, ed.). Clared on Press, Oxford, England.Google Scholar
  14. Gaffney ES, Meylan PA and Wyss AR (1991) A computer assisted analysis of the relationships of the higher categories of turtles. Cladistics 7: 313–335.CrossRefGoogle Scholar
  15. Hell TA (1999). Bioedit A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl. Acids Sym. Posit. Series 41: 95–98.Google Scholar
  16. Huelsenbeck J and Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17: 754–755.CrossRefPubMedGoogle Scholar
  17. Krenz JG, Naylor GJP, Shaffer HB and Janzen FJ (2005) Molecular phylogenetics and evolution of turtles. Mol. Phylogenet. Evol. 37: 178–191.CrossRefPubMedGoogle Scholar
  18. Kumazawa Y and Endo H (2004) Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Res. 11: 115–125.CrossRefPubMedGoogle Scholar
  19. Kumazawa Y and Nishida M (1999) Complete mitochondrial DNA sequences of the green turtle and bluetailed mole skink: statistical evidence for archoLacertilian affinity of turtles. Mol. Biol. Evol. 16: 784–792.PubMedGoogle Scholar
  20. Kumar S, Tamura k and Nei M (2004) An integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5: 150–163.CrossRefPubMedGoogle Scholar
  21. Marshall HD and Baker AJ (1998) Rates and patterns of mitochondrial DNA sequence evolution in Fringilline finches (Fringilla spp.) and the Greenfinch (Carduelis chloris). Mol. Biol. Evol. 15: 638–646.PubMedGoogle Scholar
  22. Meylan PA (1987) The phylogenetic relationships of soft-shelled turtles (family Trionychidae). Bull. Amer. Mus. Nat. Hist. 186:1–101.Google Scholar
  23. Peng QL, Pu YG, Wang ZF and Nie LW (2005) Complete mitochondrial genome sequence analysis of Chinese softshell turtle (Pelodiscus sinensis). Chin. J. Biochem. Mol. Biol. 21: 591–596.Google Scholar
  24. Posada D and Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817–818.CrossRefPubMedGoogle Scholar
  25. Randi E and Lucchini V (1998) Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J. Mol. Evol. 47: 449–462.CrossRefPubMedGoogle Scholar
  26. Ray DA and Densmore LD (2002) The crocodilian mitochondrial control region: general structure, conserved sequences and evolutionary implications. J. Exp. Zool. 294: 334–345.CrossRefPubMedGoogle Scholar
  27. Rui JL, Wang YT and Nie LW (2008) The complete mitochondrial DNA genome of Eremias brenchleyi (Reptilia: Lacertidae) and its phylogeny position within squamata reptiles. Amphibia-Reptilia 30: 25–35.CrossRefGoogle Scholar
  28. Saccone C, Pesole G and Sbisà E (1991) The main regulatory region of mammalian mitochondrial DNA: Structure function model and evolutionary pattern. J. Mol. Evol. 33: 83–91.CrossRefPubMedGoogle Scholar
  29. Sambrook J and Russell DW (2001) Molecular Cloning: A laboratory Manual. 3rd ed., Cold Spring Harbor Laboratory Press, New York.Google Scholar
  30. Sbisà E, Tanzariello F, Reyes A, Pesole G and Saccone C (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205: 125–140.CrossRefPubMedGoogle Scholar
  31. Shaffer HB, Meylan P and McKnight ML (1997) Tests of turtle phylogeny: molecular, morphological, and paleontological approaches. Syst. Biol. 46: 235–268.PubMedGoogle Scholar
  32. Southern SO, Southern PJ and Dizon AE (1988) Molecular characterizaon of a cloned dolphin mitochondrial genome. J. Mol. Evol. 28: 32–42.CrossRefPubMedGoogle Scholar
  33. Swofford DL (2002) PAUP*: Phylogenenc Analysis using Parsimony (*and Other Methods), Version 4.0b l0. Sunderland: Sinauer Associates.Google Scholar
  34. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F and Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 24: 4876–4882.CrossRefGoogle Scholar
  35. Turtle Taxonomy Working Group (2007) An annotated list of modern turtle terminal taxa with comments on areas of taxonomic instability and recent change. Chelonian Research Monographs 4: 173–199.Google Scholar
  36. Walberg MW and Clayton DA (1981) Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucl. Acids Res. 9: 5411–5421.CrossRefPubMedGoogle Scholar
  37. Yan L, Zhang Y, Wang N, Zhang L and Nie LW (2008) Comparison of Mitochondrial Control Region Sequences Between Chelydridae and Platysternidae. Zool. Res. 29: 127–133.CrossRefGoogle Scholar
  38. Zardoya R and Meyer A (1998) Cloning and characterization of a microsatellite in the mitochondrial control region of the African side-necked turtles, Pelomedusa subrufa. Gene 216: 149–153.CrossRefPubMedGoogle Scholar
  39. Zhang YY, Nie LW, Huang YQ, Pu YG and Zhang L (2009) The Mitochondrial DNA Control Region Comparation Studies of Four Hinged Turtles and Its Phylogentic Significance of the Genus Cuora sensu lato (Testudinata: Geoemydidae). Genes & Genomics 31: 349–359.CrossRefGoogle Scholar
  40. Zhang Y, Zhang E and He SP (2003) Studies on the structure of the control region of the bagridae in China and its phylogenetic significance. Acta Hydrobiol. Sinica 27: 463–467.Google Scholar
  41. Zhou T and Zhao EM (2004) The category map of Chelonia. Agriculture Press, China.Google Scholar
  42. Zhu SH, Zheng WJ, Zou JX, Yang YC and Shen XQ (2007) Mitochondrial DNA Control Region Structure and Molecular Phylogenetic Relationship of Carangidae. Zool. Res. 28: 606–614.Google Scholar

Copyright information

© The Genetics Society of Korea and Springer Netherlands 2010

Authors and Affiliations

  1. 1.Life Science CollegeAnhui Normal University, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in AnhuiWuhu, AnhuiChina

Personalised recommendations