The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

Li Zhang; Liuwang Nie; Chenghe Cao; Ying Zhan

doi:10.1016/S1673-8527(08)60005-3

Volume 35 Issue 1

Jan. 2008

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2008 > 35(1): 33-40

PDF( 390 KB)

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

doi: 10.1016/S1673-8527(08)60005-3

College of Life Sciences, Anhui Normal University, the Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu 241000, China

More Information

Corresponding author: E-mail address: lwnie@mail.ahnu.edu.cn (Liuwang Nie)
Received Date: 2007-05-28
Accepted Date: 2007-07-26
Rev Recd Date: 2007-07-26

Available Online: 2008-01-25

Publish Date: 2008-01-20

Abstract

Abstract

The complete mitochondrial genome (16,837 bp) from the Keeled box turtle (Pyxidea mouhotii) was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule: a large number of (ATTATATC) _n direct tandem repeats followed by (TA) _n microsatellite at the 3′ end of the control region (D-loop), which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood (ML) and Bayesian (BI) analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1) Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group (containing Pyxidea) may have originated from two ancestors; 2) the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.
- Pyxidea mouhotii,
- mitochondrial genome,
- control region,
- phylogenetic relationships

FullText(HTML)

References(44)

References

[1]	Avise, J.C., Bowen, B.W., Lamb, T. et al. Mitochondrial DNA evolution at a turtle's pace: Evidence for low genetic variability and reduced microevolutionary rate in the Testudines Mol. Biol. Evol., 9 (1992),pp. 457-473
[2]	Bramble, D.M Emydid shell kinesis: biomechanics and evolution Copeia, 3 (1974),pp. 707-727
[3]	Curole, A.P., Kocher, T.D. Mitogenomics: digging deeper with complete mitochondrial genomes Trends Ecol. Evol., 14 (1999),pp. 394-398
[4]	Dutton, P.H., Davis, S.K., Guerra, T. et al. Molecular phylogeny for marine turtles based on sequences of the ND4-leucine tRNA and control regions of mitochondrial DNA Mol. Phylogenet. Evol., 5 (1995),pp. 511-521
[5]	Ernst, C.H., Barbour, R.W.
[6]	Feldman, C.R., Parham, J.F. Molecular phylogenetics of emydine turtles: Taxonomic revision and the evolution of shell kinesis Mol. Phylogenet. Evol., 22 (2002),pp. 388-398
[7]	Fumagalli, L., Taberlet, P., Favre, L. et al. Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews Mol. Biol. Evol., 13 (1996),pp. 31-46
[8]	Gaffney, E.S., Meylan, P.A.
[9]	Gaffney, E.S., Meylan, P.A., Wyss, A.R. A computer assisted analysis of the relationships of the higher categories of turtles Cladistics, 7 (1991),pp. 313-335
[10]	Haiduk, M.W., and Bickham, J.W. (1982). Chromosomal homologies and evolution of testudinoid turtles with emphasis on the systematic placement of platysternon. Copeia pp. 60-66.
[11]	Hamada, H., Petrino, M.G., Kakunaga, T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes Proc. Natl. Acad. Sci. USA, 79 (1982),pp. 6465-6469
[12]	Hirayama, R. Cladistic analysis of batagurine turtles (Batagurinae: Emydidae: Testudinoidea); a preliminary results Stvd Geol Salamanticensia Vol Especial 1 Stvidia Palaeocheloniologica, 1 (1984),pp. 141-157
[13]	Hoelzel, A.R., Hancock, J.M., Dover, G.A. Generation of VNTRs and heteroplasmy by sequence turnover in the mitochondrial control region of two elephant seal species J. Mol. Evol., 37 (1993),pp. 190-197
[14]	Honda, M., Yasukawa, Y., Hirayama, R. et al. Zool. Sci., 19 (2002),pp. 1305-1312
[15]	Huelsenbeck, J., Ronquist, F. MRBAYES: Bayesian inference of phylogeny Bioinformatics, 17 (2001),pp. 754-755
[16]	IUCN
[17]	Iverson J.B. (1992). A Revised Checklist with Distribution Maps of the Turtles of the World. (Privately printed. Richmond).
[18]	Kim, I.C., Kweon, H.S., Kim, Y.J. et al. Gene, 336 (2004),pp. 147-153
[19]	Lamb, T., Lydeard, C., Gibbons, J.W. Molecular systematics of map turtles (Graptemys): A comparison of mitochondrial restriction site vs. sequence data Syst. Biol., 43 (1994),pp. 543-559
[20]	Mindell, D.P., Sorenson, M.D., Dimcheff, D.E. An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles Mol. Biol. Evol., 15 (1998),pp. 1568-1571
[21]	Mindell, D.P., Sorenson, M.D., Hasegawa, D.E. et al. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes Syst. Biol., 48 (1999),pp. 138-152
[22]	Parham, J.F., Feldman, C.R., Boore, J.L. The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): Description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA BMC. Evol. Biol., 6 (2006),p. 11
[23]	Parham, J.F., Macey, J.R., Papenfuss, T.J. et al. The phylogeny of Mediterranean tortoises and their close relatives based on complete mitochondrial genome sequences from museum specimens Mol. Phylogenet. Evol., 38 (2006),pp. 50-64
[24]	Peng, Q.L., Pu, Y.G., Wang, Z.F. et al. Chin. J. Biochem. Mol. Biol., 21 (2005),pp. 591-596
[25]	Peng, Q.L., Nie, L.W., Pu, Y.G. Gene, 380 (2006),pp. 14-20
[26]	Pu, Y.G., Peng, Q.L., Wang, Z.F. et al. Acta. Zool. Sin., 51 (2005),pp. 691-696
[27]	Sambrook, J., Russell, D.W.
[28]	Serb, J.M., Phillips, C.A., Iverson, J.B. Molecular phylogeny and biogeography of Kinosternon flavescens based on complete mitochondrial control region sequences Mol. Phylogenet. Evol., 18 (2001),pp. 149-162
[29]	Shaffer, H.B., Meylan, P., McKnight, M.L. Tests of turtles phylogeny: molecular, morphological, and paleontological approaches Syst. Biol., 46 (1997),pp. 235-268
[30]	Spinks, P.Q., Shaffer, H.B., Iverson, J.B. et al. Phylogenetic hypotheses for the turtle family Geoemydidae Mol. Phylogenet. Evol., 32 (2004),pp. 164-182
[31]	Stuart, B.L., Parham, J.F. Mol. Phylogenet. Evol., 31 (2004),pp. 164-177
[32]	Swofford, D.L.
[33]	Walberg, M.W., Clayton, D.A. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA Nucleic. Acids. Res., 9 (1981),pp. 5411-5421
[34]	Walker, D., Nelson, W.S., Buhlmann, K.A. et al. Mitochondrial DNA phylogeography and subspecies issues in the monotypic freshwater turtle Sternotherus odoratus Copeia, 1997 (1997),pp. 16-21
[35]	Walker, D., Avise, J.C. Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States Annu. Rev. Ecol. Syst., 29 (1998),pp. 23-58
[36]	Wang, H.K., Qiao, Y.S., Lou, X.M. et al. Distribution of microsatellite from complete sequence of Arabidopsis thaliana chloroplast DNA Chin. J. Biochem. Mol. Biol., 22 (2006),pp. 845-850
[37]	Whetstone, K.N Copeia (1978),pp. 159-162
[38]	Wolstenholme, D.R Animal mitochondrial DNA: structure cursor for mitochondrial genomic rearrangement Int. Rev. Cyt., 141 (1992),pp. 173-216
[39]	Wu, P., Zhou, K.Y., Yang, Q. Chin. J. Appl. Environ. Biol., 4 (1998),pp. 374-378
[40]	Wu, P., Zhou, K.Y., Yang, Q. Phylogeny of Asian freshwater and terrestrial turtles based on sequence analysis of 12S rRNA gene fragment Acta. Zool. Sin., 45 (1999),pp. 260-267
[41]	Yasukawa, Y., Hirayama, R., Hikida, T. Phylogenetic relationships of geoemydine turtles (Reptilia: Geoemydidae) Curr. Herpetol., 20 (2001),pp. 105-133
[42]	Zardoya, R., Meyer, A. Gene, 216 (1998),pp. 149-153
[43]	Zardoya, R., Meyer, A. Complete mitochondrial genome suggests diapsid affinities of turtles Proc. Natl. Acad. Sci. USA, 95 (1998),pp. 14226-14231
[44]	Zhou, T., Zhao, E.M.