A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome

Molecular Biology and Evolution

Volumn 23, Issue 1, 2006, Pages 227-234

  San Mauro, Diego ^a   Gower, David J ^b   Zardoya, Rafael ^a   Wilkinson, Mark ^b  

^a MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

Convergent rearrangement; Gene loss; Gene rearrangement; Gymnophiona; Mitochondrial genome; Tandem duplication

Indexed keywords

SPACER DNA;

AMPHIBIA; ARTICLE; CONTROLLED STUDY; GENE DUPLICATION; GENE ORDER; GENE REARRANGEMENT; MARSUPIAL; MITOCHONDRION; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROMOTER REGION; PSEUDOGENE; TANDEM REPEAT; VERTEBRATE;

AMPHIBIA; ANIMALS; BASE SEQUENCE; BAYES THEOREM; BRAZIL; DNA, INTERGENIC; DNA, MITOCHONDRIAL; GENE DELETION; GENE DUPLICATION; GENE ORDER; GENE REARRANGEMENT; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PSEUDOGENES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

AMPHIBIA; CAECILIA; GYMNOPHIONA; METATHERIA; VERTEBRATA;

EID: 28944449814     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj025     Document Type: Article

References (64)

1. Akaike, H. 1973. Information theory as an extension of the maximum likelihood principle. Pp. 267-281 in B. N. Petrov and F. Csaki, eds. Second International Symposium of Information Theory. Akademiai Kiado, Budapest, Hungary.
2. Arndt, A., and M. J. Smith. 1998. Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria. Mol. Biol. Evol. 15:1009-1016.
3. Blanchette, M., T. Kunisawa, and D. Sankoff. 1999. Gene order breakpoint in animal mitochondrial phylogeny. J. Mol. Evol. 49:193-203.
4. Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767-1780.
5. _. 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. Comparative genomics, computational biology series. Volume 1. Kluwer Academic Publishers, Dordrecht, Netherlands.
6. 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.
7. Cantatore, P., M. N. Gadaleta, M. Roberti, C. Saccone, and A. C. Wilson. 1987. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 329:853-855.
8. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
9. Cosner, M. E., R. K. Jansen, B. M. E. Moret, L.-S. Wang, T. Warnow, and S. Wyman. 2000. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. Pp. 99-121 in D. Sankoff and J. Nadeau, eds. Comparative genomics, computational biology series. Volume 1. Kluwer Academic Publishers, Dordrecht, Netherlands.
10. Darwin, C. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London.
11. Dowton, M., and A. D. Austin. 1999. Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the Hymenoptera. Mol. Biol. Evol. 16:298-309.
12. Dowton, M., L. R. Castro, and A. D. Austin. 2002. Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of the genome "morphology". Invertebr. Syst. 16:345-356.
13. Duellman, W. E., and L. Trueb. 1994. Biology of amphibians. Johns Hopkins University Press, Baltimore, Md.
14. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
15. Flook, P., H. Rowell, and G. Gellissen. 1995. Homoplastic rearrangements of insect mitochondrial tRNA genes. Naturwissenschaften 82:336-337.
16. Huelsenbeck, J. P., and F. R. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
17. Huelsenbeck, J. P., F. R. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
18. 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.
19. Jameson, D., A. P. Gibson, C. Hudelot, and P. G. Higgs. 2003. OGRe: a relational database for comparative analyses of mitochondrial genomes. Nucleic Acids Res. 31:202-206.
20. Jermiin, L., D. Graur, and R. H. Crozier. 1995. Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mtDNA. Mol. Biol. Evol. 12:558-563.
21. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
22. Kumazawa, Y., and M. Nishida. 1995. Variation in mitochondrial tRNA gene organization of reptiles as phylogentic markers. Mol. Biol. Evol. 12:759-772.
23. Kumazawa, Y., H. Ota, M. Nishida, and T. Ozawa. 1998. The complete nucleotide sequence of snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313-329.
24. Larget, B., J. B. Kadane, and D. L. Simon. 2005. A Bayesian approach to the estimation of ancestral genome arrangements. Mol. Phylogenet. Evol. 36:214-223.
25. Larget, B., D. L. Simon, J. B. Kadane, and D. Sweet. 2005. A Bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol. Evol. 22:486-495.
26. Lavrov, D. V., J. L. Boore, and W. M. Brown. 2002. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and non-random loss. Mol. Biol. Evol. 19:163-169.
27. Levinson, G., and G. A. Gutman. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:203-221.
28. Liu, Z. Q., Y. Q. Wang, and B. Su. 2005. The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate mtDNA. Gene 346:145-151.
29. Lunt, D. H., and B. C. Hyman. 1997. Animal mitochondrial DNA recombination. Nature 387:247.
30. Macey, J. R., A. Larson, N. B. Ananjeva, Z. Fang, and T. J. Papenfuss. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14:91-104.
31. Macey, J. R., T. J. Papenfuss, J. V. Kuehl, H. M. Fourcade, and J. L. Boore. 2004. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol. Phylogenet. Evol. 33:22-31.
32. Macey, J. R., J. A. Schulte II, 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.
33. Maddison, W. P., and D. R. Maddison. 1992. MacClade: analysis of phylogeny and character evolution. Sinauer Associates Inc., Sunderland, Mass.
34. Mindell, D. P., M. D. Sorenson, and D. E. Dimcheff. 1998. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 95:10693-10697.
35. Miya, M., A. Kawaguchi, and M. Nishida. 2001. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 18:1993-2009.
36. Moritz, C., and W. M. Brown. 1986. Tandem duplications of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233:1425-1427.
37. _. 1987. Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. Proc. Natl. Acad. Sci. USA 84:7183-7187.
38. Moritz, C., T. E. Dowling, and W. M. Brown. 1987. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 18:269-292.
39. Mueller, R. L., and J. L. Boore. 2005. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Mol. Biol. Evol. 22:2104-2112.
40. 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.
41. Nussbaum, R. A. 1991. Cytotaxonomy of caecilians. Pp. 22-76 in S. K. Sessions and D. M. Green, eds. Amphibian cytogenetics and evolution. Academic Press, San Diego, Calif.
42. Pääbo, S., W. K. Thomas, K. M. Whitfield, and Y. Kumazawa. 1991. Rearrangements of mitochondrial transfer RNA genes in marsupials. J. Mol. Evol. 33:426-430.
43. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
44. Robinson, M., M. Gouy, C. Gautier, and D. Mouchiroud. 1998. Sensitivity of the relative-rate test to taxonomic sampling. Mol. Biol. Evol. 15:1091-1098.
45. Robinson-Rechavi, M., and D. Huchon. 2000. RRTree: relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16:296-297.
46. Rodríguez, F., J. F. Oliver, A. Marín, and J. R. Medina. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
47. Rokas, A., and P. W. H. Holland. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15:454-459.
48. Rzhetsky, A., and M. Nei. 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945-967.
49. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
50. San Mauro, D., D. J. Gower, O. V. Oommen, M. Wilkinson, and R. Zardoya. 2004. Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Mol. Phylogenet. Evol. 33:413-427.
51. San Mauro, D., M. Vences, M. Alcobendas, R. Zardoya, and A. Meyer. 2005. Initial diversification of living amphibians pre-dated the breakup of Pangaea. Am. Nat. 165:590-599.
52. 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.
53. Seutin, G., B. F. Lang, D. P. Mindell, and R. Morais. 1994. Evolution of the WANCY region in amniote mitochondrial DNA. Mol. Biol. Evol. 11:329-340.
54. 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.
55. 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.
56. StatSoft Inc. 2001. STATISTICA (data analysis software system). (http://www.statsoft.com).
57. Swofford, D. L. 1998. PAUP *: phylogenetic analysis using parsimony (*and other methods). Version 4.0. Sinauer Associates, Inc., Sunderland, Mass.
58. Taylor, E. H. 1968. The caecilians of the world: a taxonomic analysis. University of Kansas Press, Lawrence, Kans.
59. Wilkinson, M. 1997. Characters, congruence and quality: a study of neuroanatomical and traditional data in caecilian phylogeny. Biol. Rev. 72:423-470.
60. Wilkinson, M., S. P. Loader, D. J. Gower, J. A. Sheps, and B. L. Cohen. 2003. Phylogenetic relationships of African caecilians (Amphibia: Gymnophiona): insights from mitochondrial rRNA gene sequences. Afr. J. Herpetol. 52:83-92.
61. Wilkinson, M., and R. A. Nussbaum. 1992. Taxonomic status of Pseudosiphonops ptychodermis Taylor and Mimosiphonops vermiculatus Taylor (Amphibia: Gymnophiona: Caeciliaidae) with a description of a new species. J. Nat. Hist. 26:675-688.
62. Wolstenholme, D. R. 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141:173-216.
63. Zardoya, R., and A. Meyer. 2000. Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona). Genetics 155:765-775.
64. Zhang, P., H. Zhou, D. Liang, Y. F. Liu, Y. Q. Chen, and L. H. Qu. 2005. The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians. Gene 346:133-143.