• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. Jul 15, 1992; 89(14): 6575–6579.
PMCID: PMC49544

Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome.

Abstract

Detailed knowledge of gene maps or even complete nucleotide sequences for small genomes leads to the feasibility of evolutionary inference based on the macrostructure of entire genomes, rather than on the traditional comparison of homologous versions of a single gene in different organisms. The mathematical modeling of evolution at the genomic level, however, and the associated inferential apparatus are qualitatively different from the usual sequence comparison theory developed to study evolution at the level of individual gene sequences. We describe the construction of a database of 16 mitochondrial gene orders from fungi and other eukaryotes by using complete or nearly complete genomic sequences; propose a measure of gene order rearrangement based on the minimal set of chromosomal inversions, transpositions, insertions, and deletions necessary to convert the order in one genome to that of the other; report on algorithm design and the development of the DERANGE software for the calculation of this measure; and present the results of analyzing the mitochondrial data with the aid of this tool.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.0M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Brown WM, George M, Jr, Wilson AC. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1967–1971. [PMC free article] [PubMed]
  • Sankoff D, Cedergren R, Abel Y. Genomic divergence through gene rearrangement. Methods Enzymol. 1990;183:428–438. [PubMed]
  • Nadeau JH, Taylor BA. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc Natl Acad Sci U S A. 1984 Feb;81(3):814–818. [PMC free article] [PubMed]
  • Lang BF. The mitochondrial genome of the fission yeast Schizosaccharomyces pombe: highly homologous introns are inserted at the same position of the otherwise less conserved cox1 genes in Schizosaccharomyces pombe and Aspergillus nidulans. EMBO J. 1984 Sep;3(9):2129–2136. [PMC free article] [PubMed]
  • Clark-Walker GD, McArthur CR, Sriprakash KS. Location of transcriptional control signals and transfer RNA sequences in Torulopsis glabrata mitochondrial DNA. EMBO J. 1985 Feb;4(2):465–473. [PMC free article] [PubMed]
  • Wilson C, Ragnini A, Fukuhara H. Analysis of the regions coding for transfer RNAs in Kluyveromyces lactis mitochondrial DNA. Nucleic Acids Res. 1989 Jun 26;17(12):4485–4491. [PMC free article] [PubMed]
  • Cummings DJ, McNally KL, Domenico JM, Matsuura ET. The complete DNA sequence of the mitochondrial genome of Podospora anserina. Curr Genet. 1990 May;17(5):375–402. [PubMed]
  • Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. [PubMed]
  • Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA. Sequence and gene organization of mouse mitochondrial DNA. Cell. 1981 Oct;26(2 Pt 2):167–180. [PubMed]
  • Desjardins P, Morais R. Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J Mol Biol. 1990 Apr 20;212(4):599–634. [PubMed]
  • Jacobs HT, Elliott DJ, Math VB, Farquharson A. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J Mol Biol. 1988 Jul 20;202(2):185–217. [PubMed]
  • Asakawa S, Kumazawa Y, Araki T, Himeno H, Miura K, Watanabe K. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J Mol Evol. 1991 Jun;32(6):511–520. [PubMed]
  • Smith MJ, Banfield DK, Doteval K, Gorski S, Kowbel DJ. Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus. J Mol Evol. 1990 Sep;31(3):195–204. [PubMed]
  • Clary DO, Wolstenholme DR. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol. 1985;22(3):252–271. [PubMed]
  • Wolstenholme DR, Macfarlane JL, Okimoto R, Clary DO, Wahleithner JA. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proc Natl Acad Sci U S A. 1987 Mar;84(5):1324–1328. [PMC free article] [PubMed]
  • Sankoff D, Goldstein M. Probabilistic models of genome shuffling. Bull Math Biol. 1989;51(1):117–124. [PubMed]
  • Cantatore P, Gadaleta MN, Roberti M, Saccone C, Wilson AC. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature. 329(6142):853–855. [PubMed]
  • Jacobs HT, Asakawa S, Araki T, Miura K, Smith MJ, Watanabe K. Conserved tRNA gene cluster in starfish mitochondrial DNA. Curr Genet. 1989 Mar;15(3):193–206. [PubMed]
  • Päbo S, Thomas WK, Whitfield KM, Kumazawa Y, Wilson AC. Rearrangements of mitochondrial transfer RNA genes in marsupials. J Mol Evol. 1991 Nov;33(5):426–430. [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...