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PMID: 7714909 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions.

Journal of molecular evolution ·Vol. 40 ·No. 1 ·1995-01-00 ·Pages 107-13

Mouchiroud D, Gautier C, Bernardi G

Abstract

The frequencies of synonymous substitutions of mammalian genes cover a much wider range than previously thought. We report here that the different frequencies found in homologous genes from a given mammalian pair are correlated with those in the same homologous genes from a different mammalian pair. This indicates that the frequencies of synonymous substitutions are gene-specific (as are the frequencies of nonsynonymous substitutions), or, in other words, that "fast" and "slow" genes in one mammal are fast and slow, respectively, in any other one. Moreover, the frequencies of synonymous substitutions are correlated with the frequencies of nonsynonymous substitution in the same genes.

MeSH Terms
Animals Biological Evolution Computer Simulation DNA Repair Gene Frequency Humans Mammals/genetics Models, Biological
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Mouchiroud D
Laboratoire de Biométrie, Génétique et Biologie des Populations, U.R.A. 243, Université Claude Bernard, Villeurbanne, France.
Gautier C
Bernardi G
References (37)
37 references, click to expand
  1. Mutation rates differ among regions of the mammalian genome.
    Nature. 1989 Jan 19;337(6204):283-5 PMID: 2911369
  2. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.
    Mol Biol Evol. 1985 Mar;2(2):150-74 PMID: 3916709
  3. Diversity in G + C content at the third position of codons in vertebrate genes and its cause.
    Nucleic Acids Res. 1986 Aug 26;14(16):6345-55 PMID: 3748815
  4. Gene distribution and nucleotide sequence organization in the human genome.
    Eur J Biochem. 1986 Nov 3;160(3):479-85 PMID: 3780716
  5. The isochore organization of the human genome.
    Annu Rev Genet. 1989;23:637-61 PMID: 2694946
  6. HOVERGEN: a database of homologous vertebrate genes.
    Nucleic Acids Res. 1994 Jun 25;22(12):2360-5 PMID: 8036164
  7. The distribution of genes in the human genome.
    Gene. 1991 Apr;100:181-7 PMID: 2055469
  8. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene.
    Cell. 1987 Oct 23;51(2):241-9 PMID: 3664636
  9. Codon usage changes and sequence dissimilarity between human and rat.
    J Mol Evol. 1990 Aug;31(2):81-91 PMID: 2120453
  10. Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders.
    Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):5974-8 PMID: 2068073
  11. Gene distribution and nucleotide sequence organization in the mouse genome.
    Eur J Biochem. 1986 Nov 3;160(3):469-78 PMID: 3780715
  12. Rates of nucleotide substitution are evidently higher in rodents than in man.
    Mol Biol Evol. 1987 Jan;4(1):74-82 PMID: 3128714
  13. The compositional properties of human genes.
    J Mol Evol. 1991 Jun;32(6):493-503 PMID: 1908020
  14. Evidence for higher rates of nucleotide substitution in rodents than in man.
    Proc Natl Acad Sci U S A. 1985 Mar;82(6):1741-5 PMID: 3856856
  15. High codon-usage changes in mammalian genes.
    Mol Biol Evol. 1988 Mar;5(2):192-4 PMID: 3367784
  16. Estimating the total number of nucleotide substitutions since the common ancestor of a pair of homologous genes: comparison of several methods and three beta hemoglobin messenger RNA's.
    J Mol Evol. 1980 Dec;16(3-4):153-209 PMID: 7009879
  17. DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall.
    Cell. 1985 Feb;40(2):359-69 PMID: 3838150
  18. ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage.
    Comput Appl Biosci. 1985 Sep;1(3):167-72 PMID: 3880341
  19. Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes.
    J Mol Evol. 1989 Apr;28(4):286-98 PMID: 2499685
  20. Amino acid composition and the evolutionary rates of protein-coding genes.
    J Mol Evol. 1985;22(1):53-62 PMID: 3932664
  21. The compositional distribution of coding sequences and DNA molecules in humans and murids.
    J Mol Evol. 1988;27(4):311-20 PMID: 3146641
  22. Preferential DNA repair of an active gene in human cells.
    Proc Natl Acad Sci U S A. 1986 Dec;83(23):8878-82 PMID: 3466163
  23. The isochore organization of the human genome and its evolutionary history--a review.
    Gene. 1993 Dec 15;135(1-2):57-66 PMID: 8276279
  24. DNA mismatch repair and synonymous codon evolution in mammals.
    Mol Biol Evol. 1994 Jan;11(1):88-98 PMID: 8121289
  25. Silent substitutions in mammalian genomes and their evolutionary implications.
    J Mol Evol. 1993 Dec;37(6):583-9 PMID: 8114111
  26. Mammalian gene evolution: nucleotide sequence divergence between mouse and rat.
    J Mol Evol. 1993 Oct;37(4):441-56 PMID: 8308912
  27. Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins.
    J Mol Evol. 1991 Jun;32(6):504-10 PMID: 1908021
  28. Interaction of silent and replacement changes in eukaryotic coding sequences.
    J Mol Evol. 1984-1985;21(2):161-7 PMID: 6442990
  29. A model for the correlation of mutation rate with GC content and the origin of GC-rich isochores.
    J Mol Evol. 1994 May;38(5):468-75 PMID: 8028025
  30. Global variation in G+C content along vertebrate genome DNA. Possible correlation with chromosome band structures.
    J Mol Biol. 1988 Sep 5;203(1):1-13 PMID: 3054117
  31. The structures of cytochrome c and the rates of molecular evolution.
    J Mol Evol. 1971;1(1):26-45 PMID: 4377446
  32. DNA precursor asymmetries, replication fidelity, and variable genome evolution.
    Bioessays. 1992 May;14(5):295-301 PMID: 1637360
  33. Compositional patterns in vertebrate genomes: conservation and change in evolution.
    J Mol Evol. 1988 Dec-1989 Feb;28(1-2):7-18 PMID: 3148744
  34. The mosaic genome of warm-blooded vertebrates.
    Science. 1985 May 24;228(4702):953-8 PMID: 4001930
  35. Male-driven molecular evolution: a model and nucleotide sequence analysis.
    Cold Spring Harb Symp Quant Biol. 1987;52:863-7 PMID: 3454295
  36. Why the rate of silent codon substitutions is variable within a vertebrate's genome.
    J Theor Biol. 1988 Sep 17;134(2):159-64 PMID: 3244279
  37. The vertebrate genome: isochores and evolution.
    Mol Biol Evol. 1993 Jan;10(1):186-204 PMID: 8450755
Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
Published
1995-01-00
Pages
107-13
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
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