The complete mitochondrial genome of the loggerhead turtle Caretta caretta (Testudines: Cheloniidae): Genome description and phylogenetic considerations

Mitochondrial DNA

Volumn 23, Issue 1, 2012, Pages 1-12

  Drosopoulou, Elena ^a   Tsiamis, George ^b,d   Mavropoulou, Maria ^b   Vittas, Spiros ^a,e   Katselidis, Kostas A ^b   Schofield, Gail ^c   Palaiologou, Danai ^a,f   Sartsidis, Tasos ^a   Bourtzis, Kostas ^b,d   Pantis, John ^a   Scouras, Zacharias G ^a  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^b UNIVERSITY OF IOANNINA   (Greece)

^c SWANSEA UNIVERSITY   (United Kingdom)

^d University of Western Greece   (Greece)

^e UNIVERSITY OF HEIDELBERG   (Germany)

^f UNIVERSITY OF ATHENS   (Greece)

Author keywords

individual fingerprinting; microsatellite repeats; Mitogenome; turtle phylogeny

Indexed keywords

MITOCHONDRIAL DNA; UNTRANSLATED RNA;

ARTICLE; BASE PAIRING; CARETTA CARETTA; DNA POLYMORPHISM; HETEROPLASMY; MICROSATELLITE MARKER; MITOCHONDRIAL GENOME; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; TURTLE;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; DNA, MITOCHONDRIAL; GENOME; PHYLOGENY; POLYMERASE CHAIN REACTION; TURTLES;

CARETTA CARETTA; CHELONIIDAE; TESTUDINES; VERTEBRATA;

EID: 84856633383     PISSN: 19401736     EISSN: 19401744     Source Type: Journal    
DOI: 10.3109/19401736.2011.637109     Document Type: Article

References (79)

1. Altschul SF, Gish W, MillerW, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
2. Amer SA, Kumazawa Y. 2009. Complete sequence of the mitochondrial genome of the endangered Nile soft-shelled turtle Trionyx triunguis. Egypt J Exp Biol (Zool) 5:43-50.
3. Avise JC. 1994. Molecular markers, natural history and evolution. London: Chapman and Hall.
4. Avise JC. 2007. Conservation genetics of marine turtles-ten years later. In: Hewitt D, Fulbright T, editors. Frontiers in wildlife science: Linking ecological theory and management application. Boca Raton, FL: CRC Press. p 295-314.
5. Avise JC, Bowen BW. 1994. Investigating sea turtle migration using DNA markers. Curr Opin Genet Dev 4:882-886.
6. Baldwin R, Hughes GR, Prionce RIT. 2003. Loggerhead turtles in the Indian Ocean. In: Bolten AB, Witherington BE, editors. Loggerhead sea turtles. Washington, DC: Smithsonian Books. p 218-232.
7. Barley AJ, Spinks PQ, Thomson RC, Shaffer HB. 2010. Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Mol Phylogenet Evol 55:1189-1194.
8. Bolten AB, Bjorndal KA, Martins HR, Dellinger T, Biscoito MJ, Encalada SE, Bowen BW. 1998. Transatlantic developmental migrations of loggerhead sea turtles demonstrated by mtDNA sequence analysis. Ecol Appl 8:1-7. (Pubitemid 28094399)
9. Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res 27:1767-1780. (Pubitemid 29209617)
10. Bowen BW, Abreu-Grobois FA, Balazs GH, Kamezaki N, Limpus CJ, Ferl RJ. 1995. Trans-Pacific migrations of the loggerhead turtle (Caretta caretta) demonstrated with mitochondrial DNA markers. Proc Natl Acad Sci USA 92:3731-3734.
11. Bowen BW, Avise JC, Richardson JI, Meylan AB, Margaritoulis D, Hopkins-Murphy SR. 1993a. Loggerhead turtles (Caretta caretta) in the Northwestern Atlantic Ocean and Mediterranean sea. Cons Biol 7:834-844.
12. Bowen BW, Bass AL, Chow S-M, Bostrom M, Bjorndal KA, Bolten AB, Okuyama T, Bolker BM, Epperly S, Lacasella E, Shaver D, Dodd M, Hopkins-Murphy SR, Musick JA, Swingle M, Rankin- Baransky K, Teas W, Witzell WN, Dutton PH. 2004. Natal homing in juvenile loggerhead turtles (Caretta caretta). Mol Ecol 13:3797-3808. (Pubitemid 39569055)
13. Bowen BW, Bass AL, Soares L, Toonen RJ. 2005. Conservation implications of complex population structure: Lessons from the loggerhead turtle (Caretta caretta). Mol Ecol 14:2389-2402. (Pubitemid 40902287)
14. Bowen BW, Karl SA. 2007. Population genetics and phylogeography of sea turtles. Mol Ecol 16:4886-4907. (Pubitemid 350157765)
15. Bowen BW, Nelson WS, Avise JC. 1993b. A molecular phylogeny for marine turtles: Trait mapping, rate assessment, and conservation relevance. Proc Natl Acad Sci USA 90: 5574-5577. (Pubitemid 23176203)
16. Boyle MC, FitzSimmons NN, Limpus CJ, Kelez S, Velez-Zuazo X, Waycott M. 2009. Evidence for transoceanic migrations by loggerhead sea turtles in the southern Pacific Ocean. Proc R Soc B 276:1993-1999.
17. Broderick AC, Glen F, Godely BJ, Hays GC. 2002. Estimating the number of green and loggerhead turtles nesting annually in the Mediterranean. Oryx 36:227-235. (Pubitemid 43127481)
18. Broughton RE, Milam JE, Roe BA. 2001. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 11: 1958-1967. (Pubitemid 33100437)
19. Carreras C, Pascual M, Cardona L, Aguilar A, Margaritoulis D, Rees A, Turkozan O, Levy Y, Gasith A, Aureggi M, Khalil M. 2006a. The genetic structure of the loggerhead sea turtle (Caretta caretta) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications. Conserv Genet 8:761-775. (Pubitemid 47104522)
20. Carreras C, Pont S, Maffucci F, Pascual M, Barceló A, Bentivegna F, Cardona L, Alegre F, SanFélix M, Fernández G, Aguilar A. 2006b. Genetic structuring of immature loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea reflects water circulation patterns. Mar Biol 149:1269-1279.
21. Curole AP, Kocher TD. 1999. Mitogenomics: Digging deeper with complete mitochondrial genomes. Trends Ecol Evol 14: 394-398. (Pubitemid 29428461)
22. Dodd CK, Jr. 1988. Synopsis of the biological data on the loggerhead sea turtle Caretta caretta (Linnaeus, 1758). US Fish Wildl Serv Biol Rep 88:1-110.
23. Dutton PH, Bowen BW, Owens DW, Barragan A, Davis SK. 1999. Global phylogeography of the leatherback turtle (Dermochelys coriacea). J Zool (Lond) 248:397-409. (Pubitemid 29341848)
24. Dutton PH, Davis SK, Guerra T, Owens D. 1996. Molecular phylogeny for marine turtles based on sequences of the ND4- leucine tRNA and control regions of mitochondrial DNA. Mol Phylogenet Evol 5:511-521. (Pubitemid 126320897)
25. Ehrhart LM, Bagley DA, Redfoot WE. 2003. Loggerhead turtles in the Atlantic Ocean: Geographic distribution, abundance and population status. In: Bolten AB, Witherington BE, editors. Loggerhead sea turtles. Washington, DC: Smithsonian Books. p 157-174.
26. Gaffney ES. 1975. Phylogeny of the chelydrid turtles: A study of shared derived characters in the skull. Fieldiana Geol 33: 157-178.
27. Garman S. 1880. On certain species of Chelonioidae. Bull Mus Comp Zool 6:123-126.
28. Groombridge B. 1990. Marine turtles in the Mediterranean: Distribution, population status, conservation. Nat Environ Ser (Counc Eur) 48:1-98.
29. Hatase H, Kinoshita M, Bando T, Kamezaki N, Sato K, Matsuzawa Y, Goto K, Omuta K, Nakashima Y, Takeshita H, Sakamoto W. 2002. Population structure of loggerhead turtles, Caretta caretta, nesting in Japan: Bottlenecks on the Pacific population. Mar Biol 141:299-305. (Pubitemid 36064311)
30. Hatase H, Omuta K, Tsukamoto K. 2007. Bottom or midwater: Alternative foraging behaviours in adult female loggerhead sea turtles. J Zool (Lond) 273:46-55. (Pubitemid 47300730)
31. Hawkes LA, Broderick AC, Coyne MS, Godfrey MH, Lopez-Jurado L-F, Lopez-Suarez P, Merino SE, Varo-Cruz N, Godley BJ. 2006. Phenotypically linked dichotomy in sea turtle foraging requires multiple conservation approaches. Curr Biol 16: 990-995. (Pubitemid 43744368)
32. Inoue JG, Miya M, Katsumi T, Nishida M. 2003. Evolution of the deep-sea gulper eel mitochondrial genomes: Large-scale gene rearrangements originated within the eels. Mol Biol Evol 20: 1917-1924. (Pubitemid 37420945)
33. IUCN 2011. IUCN Red List of Threatened Species. Version 2011.2. Available at: http://www.iucnredlist.org. Accessed on 14 November 2011.
34. Janke A, Arnason U. 1997. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). Mol Biol Evol 14: 1266-1272. (Pubitemid 27523140)
35. Janke A, Erpenbeck D, Nilsson M, Arnason U. 2001. The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): Implications for amniote phylogeny. Proc R Soc Lond, B, Biol Sci 268:623-631. (Pubitemid 32269851)
36. Jung S-O, Lee Y-M, Kartavtsev Y, Park I-S, Kim DS, Lee J-S. 2006. The complete mitochondrial genome of the Korean soft-shelled turtle Pelodiscus sinensis (Testudines, Trionychidae). DNA Sequence 17:471-483.
37. Kumazawa Y, Nishida M. 1999. Complete mitochondrial DNA Sequences of the green turtle and blue-tailed mole skink: Statistical evidence for Archosaurian affinity of turtles. Mol Biol Evol 16:784-792. (Pubitemid 29260832)
38. Laurent L, Casale P, Bradai MN, Godley BJ, Gerosa G, Broderick AC, Schroth W, Schierwater B, Levy AM, Freggi D, Abd el- Mawla EM, Hadoud DA, Gomati HE, Domingo M, Hadjichristophorou M, Kornaraky L, Demirayak F, Gautier CH. 1998. Molecular resolution of marine turtle stock composition in fishery bycatch: A case study in the Mediterranean. Mol Ecol 7: 1529-1542. (Pubitemid 28504068)
39. Lee PLM. 2008. Molecular ecology of marine turtles: New approaches and future directions. J Exp Mar Biol Ecol 356: 25-42.
40. Lee J-S, Miya M, Lee Y-S, Kim CG, Park E-H, Aoki Y, Nishida M. 2001. 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 280:1-7. (Pubitemid 34014878)
41. Limpus CJ, Gyuris E, Miller JD. 1988. Reassessment of the taxonomic status of the marine turtle genus Natator Mc Culloch, 1908, with a redescription of the genus and species. Trans R Soc South Aust 112:1-9.
42. Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst Biol 48: 138-152. (Pubitemid 129481129)
43. Miya M, Nishida M. 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformers): First example of transfer RNA gene rearragenements in bony fishes. Mar Biotechnol 1:416-426. (Pubitemid 30000931)
44. Monzón-Argüello C, López-Jurado LF, Rico C, Marco A, López P, Hays GC, Lee PLM. 2010. Evidence from genetic and Lagrangian drifter data for transatlantic transport of small juvenile green turtles. J Biogeogr 37:1752-1766.
45. Moore MK, Bemiss JA, Rice SM, Quattro JM,Woodley CM. 2003. Use of restriction fragment length polymorphisms to identify sea turtle eggs and cooked meats to species. Conserv Genet 4: 95-103. (Pubitemid 36590237)
46. Mueller RL, Boore JL. 2005. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Mol Biol Evol 22:2104-2112. (Pubitemid 41298079)
47. Naro-Maciel E, Le M, FitzSimmons NN, Amato G. 2008. Evolutionary relationships of marine turtles: A molecular phylogeny based on nuclear and mitochondrial genes. Mol Phylogenet Evol 49:659-662.
48. Naro-Maciel E, Reid B, Fitzsimmons NN, Le M, Desalle R, Amato G. 2010. DNA barcodes for globally threatened marine turtles: A registry approach to documenting biodiversity. Mol Ecol Resour 10:252-263.
49. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
50. Nesbø CL, Arab MO, Jakobsen KS. 1998. Heteroplasmy, length and sequence variation in the mtDNA control regions of three Percid fish species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca). Genetics 148:1907-1919. (Pubitemid 28180715)
51. Nikolaidis N, Scouras ZG. 1996. The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis. Genome 39:874-883. (Pubitemid 27039971)
52. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL. 2008. AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581-583. (Pubitemid 351256305)
53. Ojala D, Montoya J, Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470-474. (Pubitemid 11159076)
54. Palkovacs EP, Gerlach J, Caccone A. 2002. The evolutionary origin of Indian Ocean tortoises (Dipsochelys). Mol Phylogenet Evol 24: 216-227. (Pubitemid 34995915)
55. Parham JF, Feldman CR, Boore JL. 2006a. 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 6:11-21.
56. Parham JF, Macey JR, Papenfuss TJ, Feldman CR, Türkzan O, Polymeni R, Boore J. 2006b. The phylogeny of Mediterranean tortoises and their close relatives based on complete mitochondrial genome sequences from museum specimens. Mol Phylogenet Evol 38:50-64. (Pubitemid 41773273)
57. Peng QL, Nie LW, Pu YG. 2006. Complete mitochondrial genome of Chinese big-headed turtle, Platysternon megacephalum, with a novel gene organization in vertebrate mtDNA. Gene 380:14-20.
58. Pissios P, Scouras ZG. 1993. Mitochondrial DNA evolution in the montium-species subgroup of Drosophila. Mol Biol Evol 10: 375-382. (Pubitemid 23103009)
59. Posada D, Crandall KA. 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
60. Randi E, Lucchini V. 1998. Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J Mol Evol 47:449-462. (Pubitemid 28457762)
61. Ray DA, Densmore LD. 2002. The crocodilian mitochondrial control region: General structure, conserved sequences and evolutionary implications. J Exp Zool B 294:334-345. (Pubitemid 36035059)
62. Reece JS, Ehrhart LM, Parkinson CL. 2006. Mixed stock analysis of juvenile loggerheads (Caretta caretta) in Indian River Lagoon, Florida: Implications for conservation planning. Conserv Genet 7:345-352. (Pubitemid 43873289)
63. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
64. Russell DR, Beckenbach AT. 2008. Recoding of translation in turtle mitochondrial genomes: Programmed frameshift mutations and evidence of a modified genetic code. J Mol Evol 67:682-695.
65. Sbisa E, Tanzariello F, Reyes A, Graziano P, 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. (Pubitemid 28029606)
66. Schofield G, Hobson VJ, Fossette S, Lilley MKS, Katselidis KA, Hays GC. 2010. Fidelity to foraging sites, consistency of migration routes and habitat modulation of home range by sea turtles. Divers Distrib 16:840-853.
67. Shadel GS, ClaytonDA. 1997. Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66:409-435.
68. Swofford DL. 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, MA: Sinauer Associates.
69. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739.
70. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882. (Pubitemid 28022245)
71. Turtle Taxonomy Working Group [Rhodin AGJ, van Dijk PP, Iverson JB, Shaffer HB]. 2010. Turtles of the World, 2010 update: Annotated checklist of taxonomy, synonymy, distribution, and conservation status. In: Rhodin AGJ, Pritchard PVH, van Dijk PP, Saumure RA, Buhlmann KA, Iverson JB, Mittermeier RA, editors. Conservation biology of freshwater turtles and tortoises: A compilation project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group. Chelonian Research Monographs No. 5, p. 000.85-000.164, doi: 10.3854/ crm.5.000.checklist.v3.2010, http://www.iucn-tftsg.org/cbftt/.
72. van der Kuyl AC, Ballasina DLP, Dekker JT,Maas J, Willemsen RE, Goudsmit J. 2002. Phylogenetic relationships among the species of the genus Testudo (Testudines: Testudinidae) inferred from mitochondrial 12S rRNA gene sequences. Mol Phylogenet Evol 22:174-183. (Pubitemid 34973436)
73. Vittas S, Drosopoulou E, Kappas I, Pantzartzi CN, Scouras ZG. 2011. The mitochondrial genome of the European catfish, Silurus glanis (Siluriformes, Siluridae). J Biol Res-Thessalon 15:25-35.
74. Walberg MW, Clayton DA. 1981. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res 9:5411-5421.
75. Wolstenholme DR. 1992. Animal mitochondrial DNA: Structure cursor for mitochondrial genomic rearrangement. Int Rev Cyt 141:173-216. (Pubitemid 23072888)
76. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306-314. (Pubitemid 24283346)
77. Zardoya R, Meyer A. 1998. Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA 95: 14226-14231. (Pubitemid 28549349)
78. Zhang L, Nie L, Cao C, Zhang Y. 2008. The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups. J Genet Genomics 35:33-40.
79. Zuker M, Mathews DH, Turner DH. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide in RNA biochemistry and biotechnology. In: Barciszewski J, Clark BFC, editors. RNA biochemistry and biotechnology. Dordrecht, the Netherlands: Kluwer Academic Publishers. p 11-43.