The crocodilian mitochondrial control region: General structure, conserved sequences, and evolutionary implications

Journal of Experimental Zoology

Volumn 294, Issue 4, 2002, Pages 334-345

  Ray, David A ^a,b   Densmore, Llewellyn ^a  

^a TEXAS TECH UNIVERSITY   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLIGATORS AND CROCODILES; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FEMALE; MALE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ALLIGATORINAE; ANSER SP.; AVES; CROCODYLIDAE (ALL CROCODILES); GAVIALINAE; MAMMALIA; MELANOSUCHUS; PALEOSUCHUS; VERTEBRATA;

EID: 0037115476     PISSN: 0022104X     EISSN: None     Source Type: Journal    
DOI: 10.1002/jez.10198     Document Type: Conference Paper

References (45)

1. Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
2. Anderson S, de Bruijn HL, Coulson AR, Eperon IC, Sanger F, Young IG. 1982. Complete sequence of bovine mitochondrial DNA: Conserved features of the mammalian mitochondrial genome. J Mol Biol 156:683-717.
3. Bayliss P. 1987. Survey methods and monitoring within crocodile management programmes. In: Webb GJ, Manolis SC, Whitehead PJ, editors. Wildlife Management: Crocodiles and Alligators. Sydney, Australia: Surrey Beatty and Sons. p. 157-175.
4. Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res 27:1767-1780.
5. Brown GG, Gadaleta G, Pepe G, Saccone C, Sbisa E. 1986. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J Mol Biol 192:503-511.
6. Buroker NE, Brown JR, Gilbert TA, O'Hara PJ, Beckenbach AT, Thomas WK, Smith MJ. 1990. Length heteroplasmy of sturgeon mitochondrial DNA: An illegitimate elongation model. Genetics 124:157-163.
7. Chang DD, Clayton DA. 1987. A novel endonuclease cleaves at a priming site of mouse mitochondrial DNA replication. EMBO J 6:409-417.
8. Clayton DA. 1982. Replication of animal mitochondrial DNA. Cell 28:693-705.
9. Clayton DA. 1984. Transcription of the mammalian mitochondrial genome. Annu Rev Biochem 53:573-594.
10. Crochet P-A, Desmarais E. 2000. Slow rate of evolution in the mitochondrial control region of gulls (Aves: Laridae). Mol Biol Evol 12:1797-1806.
11. Desjardins P, Morais R. 1990. Sequence and gene organization of the chicken mitochondrial genome: A novel gene order in higher vertebrates. J Mol Biol 212:599-634.
12. Doda JN, Wright CT, Clayton DA. 1981. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci U S A 78:6116-6120.
13. Foran DR, Hixson JE, Brown WM. 1988. Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop synthesis. Nucleic Acids Res 16:5841-5861.
14. Gemmell NJ, Western PS, Watson JM, Marshall Graves JA. 1996. Evolution of the mammalian mitochondrial control region: Comparisons of control region sequences between monotreme and therian mammals. Mol Biol Evol 13:798-808.
15. Gorzula S, Arocha-Pinango CL, Salazar C. 1976. A method of obtaining blood by vein puncture from large reptiles. Copeia 1976:838-839.
16. Hall TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95-98.
17. 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.
18. Janke A, Gemmell NJ, Feldmaier-Fuchs G, von Haeseler A, Paabo S. 1996. The mitochondrial genome of a monotreme - The platypus (Ornithorhynchus anatinus). J Mol Evol 42:153-159.
19. Janke A, Frpenbeck D, Nilsson M, Arnason U. 2001. The mitochondrial genome of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): Implications for amniote phylogeny. Proc R Soc Lond B Biol Sci 268:623-631.
20. King TC, Low RL. 1987. Mapping of control elements in the displacement loop region of bovine mitochondrial DNA. J Biol Chem 262:6204-6213.
21. Kumar S, Tamura K, Jakobsen IB, Nei M. 2001. MEGA2: Molecular Evolutionary Genetics Analysis Software. Arizona State University, Tempe, Arizona.
22. L'Abbe DL, Duhaime J-F, Lang BF, Morais R. 1991. The transcription of DNA in chicken mitochondria initiates from one major bi-directional promoter. J Biol Chem 266:10844-10850.
23. Ludwig A, May B, Debus L, Jenneckens I. 2000. Heteroplasmy in the mtDNA control region of sturgeon. Genetics 156:1933-1947.
24. Lunt DH, Whipple LE, Hyman BC. 1998. Mitochondrial DNA variable number tandem repeats (VNTR's): Utility and problems in molecular ecology. Mol Ecol 7:1441-1455.
25. MacKay SLD, Olivo PD, Laipis PJ, Hauswirth WW. 1986. Template-directed arrest of mammalian mitochondrial DNA synthesis. Mol Cell Biol 6:1261-1267.
26. Marshall HD, 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.
27. Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911-940.
28. Matson CW, Baker RJ. 2001. DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys). Mol Biol Evol 18:1494-1501.
29. Mindell DP, Knight A, Baer C, Huddleston CJ. 1996. Slow rates of molecular evolution in birds and the metabolic rate and body temperature hypotheses. Mol Biol Evol 13:422-426.
30. Poe S. 1996. Data set incongruence and the phylogeny of the crocodilians. Syst Biol 45:393-414.
31. Quinn TW, Mindell DP. 1996. Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara. Mol Phylogenet Evol 5:344-351.
32. Quinn TW, Wilson AC. 1993. Sequence evolution in and around the mitochondrial control region in birds. J Mol Evol 37:417-425.
33. Randi E, Lucchini V. 1998. Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J Mol Evol 47:449-162.
34. Randi E, Lucchini V, Hennache A, Kimball RT, Braun EL, Ligon DL. 2000. Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Mol Phylogenet Evol 19:187-201.
35. Ritchie PA, Lambert DM. 2000. A repeat complex in the mitochondrial control region of Adelie penguins from Antarctica. Genome 43:613-618.
36. Roe BA, Ma D-P, Wilson RK, Wong JF-H. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem 260:9759-9774.
37. Sbisa E, Tanzariello F, Reyes A, Pesole G, 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.
38. Swofford DL. 1998. PAUP (Phylogenetic Analysis Using Parsimony), Version 4.01b.
39. 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 24:4876-4882.
40. 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.
41. White PS, Tatum OL, Tegelstrom H, Densmore LD III. 1998. Mitochondrial DNA isolation separation and detection of fragments. In: Hoelzel AR, editor. Molecular Genetic Analysis of Populations: A Practical Approach. New York: Oxford University Press. p 65-101.
42. Wilkinson GS, Chapman AM. 1991. Length and sequence variation in evening bat D-loop mtDNA. Genetics 128:607-617.
43. Wong TW, Clayton DA. 1985. In vitro replication of human mitochondrial DNA: Accurate initiation at the origin of light-strand synthesis. Cell 42:951-958.
44. Zardoya R, Meyer A. 1998. Cloning and characterization of a microsatellite in the mitochondrial control region of the African side-necked turtle, Pelomedusa subrufa. Gene 216:149-153.
45. Zhu D, Jamieson BGM, Hugall A, Moritz C. 1994. Sequence evolution and phylogenetic signal in D-loop and cytochrome b sequences of rainbow fishes (Melanotaeniidae). Mol Biol Evol 11:672-683.