Structure and patterns of sequence variation in the mitochondrial DNA control region of the great cats

Mitochondrion

Volumn 1, Issue 3, 2001, Pages 279-292

  Jae Heup, Kim ^a   Eizirik, E ^a   O'Brien, S J ^a   Johnson, W E ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Control region; Felidae; Heteroplasmy; Mitochondrial DNA; Panthera genus; Phylogenetic analyses

Indexed keywords

ANIMALIA; FELIDAE; FELIS CATUS; PANTHERA; PANTHERA LEO; PANTHERA ONCA; PANTHERA PARDUS;

EID: 0040374468     PISSN: 15677249     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1567-7249(01)00027-7     Document Type: Article

References (64)

1. Anderson S., Bankier A.T., Barrell B.G., et al. Sequence and organization of the human mitochondrial genome. Nature. 290:1981;457-465.
2. Andrews R.M., Kubacka I., Chinnery P.F., Lightowlers R.N., Turnbull D.M., Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23:1999;147.
3. Aquadro C.F., Greenberg B.D. Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics. 103:1983;287-312.
4. Arnason E., Rand D.M. Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua. Genetics. 132:1992;211-220.
5. Avise J.C. Molecular Markers, Natural History and Evolution. 1994;Chapman and Hall, New York.
6. Beckman K.B., Smith M.F., Orrego C. Purification of Mitochondrial DNA with Wizard Minipreps DNA Purification System. Promega Note. 1993;10-13.
7. Brown W.M. The mitochondrial genome of animals. Macintyre R.J. Molecular Evolutionary Genetics. 1985;95-130 Plenum Press, New York.
8. Brown J.R., Beckenbach A.T., Smith M.J. Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus). Mol. Biol. Evol. 10:1993;326-341.
9. Buroker N.E., Brown J.R., Gilbert T.A., Ohara P.J., Beckenbach A.T., Thomas W.K., Smith M.J. Length heteroplasmy of sturgeon mitochrondrial-DNA, An illegitimate elongation model. Genetics. 124:1990;157-163.
10. Byrne E., Trounce I., Marzuki S., et al. Functional respiratory chain studies in mitochondrial cytopathies: support for mitochondrial DNA heteroplasmy in myoclonus epilepsy and ragged red fibers syndrome. Acta Neuropathol. 81:1991;318-323.
11. Casane D., Dennebouy N., de Rochambeau H., Mounolou J.C., Monnerot M. Nonneutral evolution of tandem repeats in the mitochondrial DNA control region of Lagomorphs. Mol. Biol. Evol. 14:1997;779-789.
12. Chang D.D., Clayton D.A. Priming of mammalian mitochondrial DNAs begins at the light strand promoter. Proc. Natl. Acad. Sci. USA. 82:1985;351-355.
13. Chang D.D., Clayton D.A. Identification of primary transcription start sites of mouse mitochondrial DNA: accurate in vitro initiation of both heavy- and light-strand transcriptions. Mol. Cell. Biol. 6:1986;1446-1453.
14. Clayton D.A. Replication of animal mitochondrial DNA. Cell. 28:1982;693-705.
15. Clayton D.A. Transcription and replication of animal mitochondrial DNAs. Int. Rev. Cytol. 141:1992;217-232.
16. Desjardins P., Morais R. Sequence and gene organization of the chicken mitochondrial genome, a novel gene order in higher vertebrates. J. Mol. Biol. 212:1990;599-634.
17. Doda J.N., Wright C.T., Clayton D.A. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc. Natl. Acad. Sci. USA. 78:1981;6116-6170.
18. Eizirik E., Bonatto S.L., Johnson W.E., et al. Phylogeographic patterns and evolution of the mitochondrial DNA control region in two neotropical cats (Mammalia, Felidae). J. Mol. Evol. 47:1998;613-624.
19. Engels, B., 1997. Amplify: Software for PCR, version 2.53B. University of Wisconsin, WI.
20. Gemmell N.J., Western P.S., Watson J.M., Graves J.A. Evolution of the mammalian mitochondrial control region - comparisons of control region sequences between monotreme and therian mammals. Mol. Biol. Evol. 13:1996;798-808.
21. Ghivizzani S.C., Mackay S.L.D., Madsen C.S., Laipis P.J., Hauswirth W.W. Transcribed heteroplasmic repeated sequences in the porcine mitochondrial DNA D-loop region. J. Mol. Evol. 37:1993;36-47.
22. Hamazaki S., Koshiba M., Sugiyama T. Organ distribution of mutant mitochondrial tRNA Aleu (UUR) gene in a MELAS patient. Acta Pathol. Jpn. 43:1993;187-191.
23. Harrison R.G. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol. Evol. X:1989;6-11.
24. Hayasaka K., Ishida T., Horai S. Heteroplasmy and polymorphism in the major noncoding region of mitochondrial-DNA in Japanese monkeys, association with tandemly repeated sequences. Mol. Biol. Evol. 8:1991;399-415.
25. Hoelzel A.R., Dover G.A. Evolution of the cetacean mitochondrial D-loop region. Mol. Biol. Evol. 8:1991;475-493.
26. Hoelzel A.R., Lopez J.V., Dover G.A., O'Brien S.J. Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J. Mol. Evol. 39:1994;191-199.
27. Holland M.M., Parsons T.J. Mitochondrial DNA sequence analysis - validation and use for forensic casework. Forensic Sci. Rev. 11:1999;22-50.
28. Howell N., Xu M., Halvorson S., Bodis-Wollner I., Sherman J. A heteroplasmic LHON family: tissue distribution and transmission of the 11778 mutation. Am. J. Hum. Genet. 55:1994;203.
29. Hurko O., Johns D.R., Rutledge S.L., et al. Heteroplasmy in chronic external ophthalmoplegia: clinical and molecular observations. Pediatr. Res. 28:1990;542.
30. Jacobs H.T., Holt I.J. The mitochondrial genetic system. Singh K.K. Mitochondrial DNA Mutations in Aging, Disease and Cancer. 1998;43-84 Springer, New York.
31. Johnson W.E., O'Brien S.J. Phylogenetic reconstruction of the Felidae using 16S rRNA and NADH-5 mitochondrial genes. J. Mol. Evol. 44:1997;S98-S116.
32. Johnson W.E., Dratch P.A., Martenson J.S., O'Brien S.J. Resolution of recent radiations within three evolutionary lineages of Felidae using mitochondrial restriction fragment length polymorphism variation. J. Mamm. Evol. 3:1996;97-120.
33. King T.C., Low R.L. Mitochondrial DNA displacement loop structure depends on growth state in bovine cells. J. Biol. Chem. 262:1987;6214-6220.
34. Kocher T.D., Thomas W.K., Meyer A., et al. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA. 86:1989;6196-6200.
35. Kumar S., Tamura K., Nei M. MEGA: Molecular Evolutionary Genetic Analysis. 1993;The Pennsylvania State University, University Park, PA.
36. Kumar S., Suzuki H., Onoue S., Suzuki S., Hattori N. Rat mitochondrial mtDNA-binding proteins to inter-specifically conserved sequences in the displacement loop region of vertebrate mtDNAs. Biochem. Mol. Biol. Int. 36:1995;973-981.
37. Li W.H. Molecular Evolution. 1991;Sinauer Associates, Sunderland, MA.
38. Lopez J.V., Yuhki N., Masuda R., Modi W., O'Brien S.J. Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J. Mol. Evol. 39:1994;174-190.
39. Lopez J.V., Cevario S., O'Brien S.J. Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics. 33:1996;229-246.
40. Lopez J.V., Culver M., Stephens J.C., Johnson W.E., O'Brien S.J. Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Mol. Biol. Evol. 14:1997;277-286.
41. Macmillan C., Lach B., Shoubridge E.A. Variable distribution of mutant mitochondrial DNAs (tRNA Leu[3243]) in tissues of symptomatic relative with MELAS: the role of mitotic segregation. Neurology. 43:1993;1586-1590.
42. Matthews P.M., Hopkins J., Brown R.M., Stephenson J.B.P., Hilton-Jones D., Brown G.K. Comparison of the relative levels of the 3243 (A→G) mtDNA mutation in heteroplasmic adult and fetal tissues. J. Med. Genet. 31:1994;41-44.
43. Michikawa Y., Mazzucchelli F., Bresolin N., Scrlato G., Attardi G. Aging-dependent large accumulation of point mutations in the human mtDNA control region for replication. Science. 286:1999;774-779.
44. Mignotte F., Gueride M., Champagne A.-M., Mounolou J.-C. Direct repeats in the non-coding region of rabbit mitochondrial DNA. Eur. J. Biochem. 194:1990;561-571.
45. Moritz C., Dowling T.E., Brown W.M. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 18:1987;269-292.
46. Nilsen H., Otterlei M., Haug T., et al. Nuclear and mitochondrial uracil-DNA glycocylases are generated by alternative splicing and transcription from different positions in the UNG gene. Nucleic Acids Res. 25:1997;750-755.
47. Ohno K., Tanaka M., Suzuki H., Ohbayashi T., Ikebe S. Identification of a possible control element, Mt5, in the major noncoding region of mitochondrial DNA by intraspecific nucleotide conservation. Biochem. Int. 24:1991;263-271.
48. Pecon Slattery J., O'Brien S.J. Patterns of Y and X chromosome DNA sequence divergence during the Felidae radiation. Genetics. 148:1998;1245-1255.
49. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
50. Savolainen P., Arvestad L., Lundeberg J. mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats. Mol. Biol. Evol. 17:2000;474-488.
51. Sbisa E., Tanzariello F., Reyes A., Pesole G., Saccone C. Mammalian mitochondrial D-loop structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene. 205:1997;125-140.
52. Schmitz J., Ohme M., Zischler H. The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of Scandentia to other Eutherian orders. Mol. Biol. Evol. 17:2000;1334-1343.
53. Solignac M., Gebnermont J., Monnerot M., Mounolou J.C. Drosophila mitochondrial genetics: evolution of heteroplasmy through germ line cell divisions. Genetics. 117:1987;687-696.
54. Stacy J.E., Jarde P.E., Steen H., Ims R.A., Puvis A., Jakobsen K.S. Lack of concordance between mtDNA gene flow and population density fluctuations in the bank vole. Mol. Ecol. 6:1997;751-759.
55. Steighner R.J., Holland M. Amplification and sequencing of mitochondrial DNA in forensic casework. Methods Mol. Biol. 98:1998;213-223.
56. Stoneking M., Hedgecock D., Higuchi R.G., Vigilant L., Erlich H.A. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am. J. Hum. Genet. 48:1991;370-382.
57. Swofford D.L. PAUP*, Version 4.0. 1998;Sinauer, Sunderland, MA.
58. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The Clustal-X windows interface: flexible strategies for multiple alignment aided by quality analysis tools. Nucleic Acids Res. 25:1997;4876-4882.
59. Turner, A., 1996. The big cats and their fossil relatives, Columbia University Press, New York, NY.
60. Underhill P.A., Jin L., Lin A.A., et al. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 10:1997;996-1005.
61. Wallace D.C. Mitochondrial genes and disease. Hosp. Pract. 21:1986;77-92.
62. Wilkinson G.S., Chapman A.M. Length and sequence variation in Evening Bat D-loop mtDNA. Genetics. 128:1991;607-617.
63. Wilkinson G.S., Mayer F., Kerth G., Petri B. Evolution of repeated sequence arrays in the d-loop region of bat mitochondrial DNA. Genetics. 147:1997;1035-1048.
64. Yang Y.G., Lin Y.S., Wu J.L., Hui C.F. Variation in mitochondrial DNA and population structure of the Taipei treefrog Rhacophorus taipeianus in Taiwan. Mol. Ecol. 3:1994;219-228.