Abstract
One model for gene rearrangement specifies that a portion of the genome is duplicated, followed by the random loss of the now supernumerary genes. Depending on which genes are lost, this process may reorder the duplicated block of genes. Comparisons of mitochondrial genomes have many advantages for addressing the processes of molecular evolution, including gene rearrangement. Here is an analysis of those variations in mitochondrial gene arrangement observed so far among the best sampled group, the deuterostome animals. The duplication/ random loss model is invoked to potentially reconstruct many, though not all, of these rearrangements.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Arndt, A. and Smith, M. J. 1998. Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria. Molecular Biology and Evolution 15:1009–1016.
Awadalla, P., Eyre-Walker, A., and Smith, J. M. 1999. Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286:2524–2525.
Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Research 27:1767–1780.
Boore, J. L. and Brown, W. M. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics and Development 8:668–674.
Boore, J. L. and Brown, W. M. 2000. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Molecular Biology and Evolution 17:87–106.
Boore, J. L., Collins, T. M., Stanton, D., Daehler, L. L., and Brown, W. M. 1995. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 376:163–165.
Boore, J. L., Daehler, L. L., and Brown, W. M. 1999. Complete sequence, gene arrangement and genetic code of mitochondrial DNA from the cephalochordate Branchiostoma floridae (“amphioxus”). Molecular Biology and Evolution 16:410–418.
Boore, J. L., Lavrov, D., and Brown, W. M. 1998. Gene translocation links insects and crustaceans. Nature 392:667–668.
Brusca, R. C. and Brusca, G. J. 1990. Invertebrates. Sinaeur, Sunderland, MA.
Clary, D. O. and Wolstenholme, D. R. 1985. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. Journal of Molecular Evolution 22:252–271.
Hoffmann, R. J., Boore, J. L., and Brown, W. M. 1992. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131:397–412.
Kumazawa, Y. and Nishida, M. 1995. Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Molecular Biology and Evolution 12:759–772.
Kumazawa, Y., Ota, H., Nishida, M., and Ozawa, T. 1996. Gene rearrangements in snake mitochondrial genomes: Highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Molecular Biology and Evolution 13:1242–1254.
Kumazawa, Y., Ota, H., Nishida, M., and Ozawa, T. 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313–329.
Lee, W.-J. and Kocher, T. 1995. Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization. Genetics 139:873–887.
Lunt, D. H. and Hyman, B. C. 1997. Animal mitochondrial DNA recombination. Nature 387:247.
Macey, J. R., Larson, A., Ananjeve, N. B., and Papenfuss, T. 1997. Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards. Journal of Molecular Evolution 44:660–674.
Macey, J. R., Schulte, J. A., Ananjeve, N. B., Larson, A., Rastegar-Pouyani, N., Shammakov, S. M., and Papenfuss, T. 1998a. Phylogenetic relationsips among agamid lizards of the Laudakia caucasia species group: Testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian plateau. Molecular Phylogenetics and Evolution 10:118–131.
Macey, J. R., Schulte, Ii.J. A., Larson, A., and Papenfuss, T. 1998b. Tandem duplication via light-strand synthesis may provide a precursor for mitochondrial genomic rearrangement. Molecular Biology and Evolution 15:71–75.
Mindell, D., Sorenson, M. D., and Dimcheff, D. E. 1998. Multiple independent origins of mitochondrial gene order in birds. Proceedings of the National Academy of Sciences USA 95:10693–10697.
Quinn, T. W. and Mindell, D. P. 1996. Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara. Molecular Phylogenetics and Evolution 5:344–351.
Raimond, R., Marcadé, I., Bouchon, D., Rigaud, T., Bossy, J.-P., and Souty-Grosset, C. 1999. Organization of the large mitochondrial genome in the isopod Armadillidiurn vulgare. Genetics 151:203–210.
Smith, M. J., Arndt, A., Gorske, S., and Fajber, E. 1993. The phylogeny of echinoderm classes based on mitochondrial gene arrangements. Journal of Molecular Evolution 36:545–554.
Stanton, D. J., Daehler, L. L., Moritz, C. C., and Brown, W. M. 1994. Potential stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA. Genetics 137:233–241.
Yamazaki, N., Ueshima, R., Terrett, J., Yokobori, S.-L, Kaifu, M., Segawa, R., Kobayashi, T., Numachi, K.-L, Ueda, T., Nishikawa, K., Watanabe, K., and Thomas, R. 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.
Yokobori, S.-I., Takuya, U., Feldmaier-Fuchs, G., Pääbo, S., Ueshima, R., Kondow, A., Nishikawa, K., and Watanabe, K. 1998. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochor-data). Genetics 153:1851–1862.
Yoneyama, Y. 1987. The nucleotide sequences of the heavy and light strand replication origins of the Rana catesbeiana mitochondrial genome. Nippon Ika Daigaku Zasshi 54:429–440.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2000 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Boore, J.L. (2000). The Duplication/Random Loss Model for Gene Rearrangement Exemplified by Mitochondrial Genomes of Deuterostome Animals. In: Sankoff, D., Nadeau, J.H. (eds) Comparative Genomics. Computational Biology, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4309-7_13
Download citation
DOI: https://doi.org/10.1007/978-94-011-4309-7_13
Publisher Name: Springer, Dordrecht
Print ISBN: 978-0-7923-6584-6
Online ISBN: 978-94-011-4309-7
eBook Packages: Springer Book Archive