Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders

Molecular Biology and Evolution

Volumn 22, Issue 10, 2005, Pages 2104-2112

  Mueller, Rachel Lockridge ^a,b,c   Boore, Jeffrey L ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

Complete mitochondrial genomes; Gene rearrangement; Plethodontids; Pseudogenes; Tandem duplication

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; GENE DUPLICATION; GENE REPLICATION; GENE SEQUENCE; GENOMICS; MITOCHONDRION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; SALAMANDER;

ANIMALS; CHROMOSOME MAPPING; DNA, MITOCHONDRIAL; GENE REARRANGEMENT; GENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; URODELA;

CAUDATA; PLETHODONTIDAE;

EID: 24744442601     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi204     Document Type: Article

References (50)

1. Arndt, A., and M. J. Smith. 1998. Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria. Mol. Biol. Evol. 15:1009-1016.
2. Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767-1780.
3. _. 2000. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. Pp. 133-147 in D. Sankoff and J. Nadeau, eds. Computational biology series, Vol. 1. Kluwer Academic Publishers, Dordrecht, Netherlands.
4. Boore, J. L., and W. M. Brown. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8:668-674.
5. Boore, J. L., M. Medina, and L. A. Rosenberg. 2004. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol. Biol. Evol. 21:1492-1503.
6. Delarbre, C., A.-S. Rasmussen, U. Arnason, and G. Gachelin. 2001. The complete mitochondrial genome of the hagfish Myxine glutinosa: unique features of the control region. J. Mol. Evol. 53:634-641.
7. Densmore, L. D., J. W. Wright, and W. M. Brown. 1985. Length variation and heteroplasmy are frequent in mitochondrial DNA from parthenogenetic and bisexual lizards (genus Cnemidophorus). Genetics 110:689-707.
8. Desjardins, P., and R. Morais. 1990. Sequence and gene organization of the chicken mitochondrial genome: a novel gene order in higher vertebrates. J. Mol. Biol. 212:599-634.
9. DiMauro, S., and E. A. Schon. 2003. Mitochondrial respiratory-chain diseases. N. Engl. J. Med. 348:2656-2668.
10. Dowton, M., and A. D. Austin. 1999. Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the hymenoptera. Mol. Biol. Evol. 16:298-309.
11. Dowton, M., and N. J. H. Campbell. 2001. Intramitochondrial recombination: is it why some mitochondrial genes sleep around? Trends Ecol. Evol. 16:269-271.
12. Dowton, M., L. R. Castro, S. L. Campbell, S. D. Bargon, and A. D. Austin. 2003. Frequent mitochondrial gene rearrangements at the hymenopteran nad3-nad5 junction. J. Mol. Evol. 56: 517-526.
13. Eberhard, J. R., T. F. Wright, and E. Bermingham. 2001. Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Mol. Biol. Evol. 18: 1330-1342.
14. Feder, M. E. 1976. Lunglessness, body size, and metabolic rate in salamanders. Physiol. Zool. 49:398-406.
15. Gregory, T. R. 2003. Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approach to the C-value enigma. Biol. J. Linn. Soc. 79: 329-339.
16. Holt, I. J., D. R. Dunbar, and H. T. Jacobs. 1997. Behaviour of a population of partially duplicated mitochondrial DNA molecules in cell culture: segregation, maintenance and recombination dependent upon nuclear background. Hum. Mol. Genet. 6:1251-1260.
17. Inoue, J. G., M. Miya, K. Tsukamoto, and M. Nishida. 2003. Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels. Mol. Biol. Evol. 20:1917-1924.
18. Kajander, O. A., A. T. Rovio, K. Majamaa, J. Poulton, J. N. Spelbrink, I. J. Holt, P. J. Karhunen, and H. T. Jacobs. 2000. Human mtDNA sublimons resemble rearranged mitochondrial genoms found in pathological states. Hum. Mol. Genet. 9:2821-2835.
19. Kumazawa, Y., H. Ota, M. Nishida, and T. Ozawa. 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313-329.
20. Lee, J.-S., M. Miya, Y.-S. Lee, C. G. Kim, E.-H. Park, Y. Aoki, and M. Nishida. 2001. The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish. Gene 280:1-7.
21. Lunt, D. H., and B. C. Hyman. 1997. Animal mitochondrial DNA recombination. Nature 387:247.
22. Macey, J. R., A. Larson, N. B. Ananjeva, Z. Fang, and T. J. Papenfuss. 1997a. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14:91-104.
23. Macey, J. R., A. Larson, N. B. Ananjeva, and T. J. Papenfuss. 1997b. Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Mol. Biol. Evol. 14:30-39.
24. Macey, J. R., J. A. Schulte II, and A. Larson. 2000. Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Syst. Biol. 49:257-277.
25. Macey, J. R., J. A. I. Schulte, A. Larson, and T. J. Papenfuss. 1998. Tandem duplication via light-strand synthesis may provide a precursor for mitochondrial genomic rearrangement. Mol. Biol. Evol. 15:71-75.
26. McKnight, M. L., and H. B. Shaffer. 1997. Large, rapidly evolving intergenic spacers in the mitochondrial DNA of the salamander family Ambystomatidae (Amphibia: Caudata). Mol. Biol. Evol. 14:1167-1176.
27. Miller, A. D., T. T. T. Nguyen, C. P. Burridge, and C. M. Austin. 2004. Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene 331:65-72.
28. Moore, C. A., J. Gudikote, and G. C. Van Tuyle. 1998. Mitochondrial DNA rearrangements, including partial duplications, occur in young and old rat tissues. Mutat. Res. 421:205-217.
29. Moritz, C. 1991. Evolutionary dynamics of mitochondrial DNA duplications in parthenogenetic geckos, Heteronotia binoei. Genetics 129:221-230.
30. Moritz, C., T. E. Dowling, and W. M. Brown. 1987. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Ann. Rev. Ecol. Syst. 18:269-292.
31. Moritz, C., and W. M. Brown. 1986. Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233:1425-1427.
32. _. 1987. Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. Proc. Natl. Acad. Sci. USA 84:7183-7187.
33. Mueller, R. L., J. R. Macey, M. Jaekel, D. B. Wake, and J. L. Boore. 2004. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc. Natl. Acad. Sci. USA 101:13820-13825.
34. Pääbo, S., W. K. Thomas, K. M. Whitfield, Y. Kumazawa, and A. C. Wilson. 1991. Rearrangements of mitochondrial transfer RNA genes in marsupials. J. Mol. Evol. 33:426-430.
35. Quinn, T. W., and D. P. Mindell. 1996. Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara. Mol. Phylogenet. Evol. 5:344-351.
36. Sankoff, D., G. Leduc, N. Antoine, B. Paquin, B. F. Lang, and R. Cedergren. 1992. Gene order comparisons for phylogenetic inference evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. USA 89:6575-6579.
37. Selosse, M.-A., B. Albert, and B. Godelle. 2001. Reducing the genome size of organelles favours gene transfer to the nucleus. Trends Ecol. Evol. 16:135-141.
38. Shadel, G. S., and D. A. Clayton. 1997. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66:409-435.
39. Shao, R., N. J. H. Campbell, E. R. Schmidt, and S. C. Barker. 2001. Increased rate of gene rearrangement in the mitochondrial genomes of three orders of hemipteroid insects. Mol. Biol. Evol. 18:1828-1832.
40. Smith, M. J., D. K. Banfield, K. Doteval, S. Gorski, and D. J. Kowbel. 1989. Gene arrangement in sea star mitochondrial DNA demonstrates a major inversion event during echinoderm evolution. Gene 76:181-185.
41. Stanton, D. J., L. L. Daehler, C. C. Moritz, and W. M. Brown. 1994. Sequences with the potential to form stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA. Genetics 137:233-241.
42. Tang, Y., G. Manfredi, M. Hirano, and E. A. Schon. 2000a. Maintenance of human rearranged mitochondrial DNAs in long-term cultured transmitochondrial cell lines. Mol. Biol. Cell 11:2349-2358.
43. Tang, Y., E. A. Schon, E. Wilichowski, M. E. Vazquez-Memije, E. Davidson, and M. P. King. 2000b. Rearrangements of human mitochondrial DNA (mtDNA): new insights into the regulation of mtDNA copy number and gene expression. Mol. Biol. Cell 11:1471-1485.
44. Townsend, J. P., and D. M. Rand. 2004. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity 93:98-103.
45. Wallis, G. P. 1987. Mitochondrial DNA insertion polymorphism and germ line heteroplasmy in the Triturus cristatus complex. Heredity 58:229-238.
46. Yamazaki, N., R. Ueshima, J. A. Terrett et al. (12 co-authors). 1997. Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics 145:749-758.
47. Yokobori, S.-I., N. Fukuda, M. Nakamura, T. Aoyama, and T. Oshima. 2004. Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes. Mol. Biol. Evol. 21:2034-2046.
48. Zardoya, R., E. Malaga-Trillo, M. Veith, and A. Meyer. 2003. Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani. Gene 317:17-27.
49. Zhang, P., Y.-Q. Chen, Y.-F. Liu, H. Zhou, and L.-H. Qu. 2003a. The complete mitochondrial genome of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata). Gene 311:93-98.
50. Zhang, P., Y.-Q. Chen, H. Zhou, X.-L. Wang, and L.-H. Qu. 2003b. The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny. Mol. Phylogenet. Evol. 28:620-626.