Impact of changes in GC content on the silent molecular clock in murids

Gene

Volumn 205, Issue 1-2, 1997, Pages 317-322

  Mouchiroud, Dominique ^a   Robinson, Marc ^a   Gautier, Christian ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

Base composition; Codon usage; GC homogenization; Isochores; Molecular clock; Murid genomes; Regional mutational pressure; Stationarity

Indexed keywords

DNA BASE;

CATTLE; CODON USAGE; CONFERENCE PAPER; DNA BASE COMPOSITION; EVOLUTION; HUMAN; ISOCHORE; MOUSE; MUTATION RATE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; RAT; SWINE;

ANIMALS; CATTLE; CYTOSINE; EVOLUTION, MOLECULAR; GENOME; GUANINE; HUMANS; MURIDAE;

BOS TAURUS; BOVINAE; MAMMALIA; MURIDAE; RODENTIA; SUS SCROFA;

EID: 0031593217     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(97)00480-0     Document Type: Conference Paper

References (32)

1. Bernardi, G., Bernardi, G., 1986. Compositional constraint and genome evolution. J. Mol. Evol. 24, 1-11.
2. Bernardi, G., Mouchiroud, D., Gautier, C., Bernardi, G., 1988. Compositional patterns in vertebrate genomes: conservation and change in evolution. J. Mol. Evol. 28, 7-18.
3. Bernardi, G., Mouchiroud, D., Gautier, C., 1993. Silent substitutions in mammalian genomes and their evolutionary implications. J. Mol. Evol. 37, 583-589.
4. Bernardi, G., 1995. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29, 445-476.
5. Britten, R.J., 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science 231, 1393-1398.
6. Bulmer, M., Wolfe, K.H., Sharp, P.M., 1991. Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders. Proc. Natl. Acad. Sci. USA 88, 5974-5978.
7. Cacciò S., Perani, P., Saccone, S., Kadi, F., Bernardi, G., 1994. Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates. J. Mol. Evol. 39, 331-339.
8. Catzeflis, F.M., Sheldon, F.H., Ahlquist, J.E., Sibley, C.G., 1987. DNA-DNA hybridization evidence of the rapid rate of muroid rodent DNA evolution. Mol. Biol. Evol. 4, 242-253.
9. Duret, L., Mouchiroud, D., Gouy, M., 1994. HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res. 22, 2360-2363.
10. Filipski, J., 1987. Correlation between molecular clock ticking, codon usage, fidelity of DNA repair, chromosome banding and chromatin compactness in germline cells. FEBS Lett. 217, 184-186.
11. Filipski, J., 1990. Evolution of DNA sequence contributions of mutational bias and selection to the origin of chromosomal compartments. Adv. Mutagen. Res. 2, 1-54.
12. Hanawalt, P.C., 1991. Heterogeneity of DNA repair at the gene level. Mutat. Res. 247, 203-211.
13. Holmquist, G.P., Filipski, J., 1994. Organization of mutations along the genome: a prime determinant of genome evolution. TREE 9, 65-69.
14. Galtier, N., Gouy, M., 1995. Inferring phylogenies from DNA sequences of unequal base compositions. Proc. Natl. Acad. Sci. USA 92, 11317-11321.
15. Koop, B.F., 1995. Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution. Trends Genet. 11, 367-371.
16. Li, W.H., Wu, C., Luo, C., 1985. A new method for estimating synonymous and non-synonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codons changes. Mol. Biol. Evol. 2, 150-174.
17. Mellon, I., Spivak, G., Hanawalt, P.C., 1987. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell 51, 241-249.
18. Mouchiroud, D., Gautier, C., 1988. High codon usage changes in mammalian genes. Mol. Biol. Evol. 5, 192-194.
19. Mouchiroud, D., Gautier, C., Bernardi, G., 1988. The compositional distribution of coding sequences and DNA molecules in humans and murids. J. Mol. Evol. 27, 311-320.
20. Mouchiroud, D., Gautier, C., 1990. Codon usage changes and sequence dissimilarity between human and rat. J. Mol. Evol. 31, 81-91.
21. Mouchiroud, D., Bernardi, G., 1993. Compositional properties of coding sequences and mammalian phylogeny. J. Mol. Evol. 37, 109-116.
22. Mouchiroud, D., Gautier, C., Bernardi, G., 1995. Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J. Mol. Evol. 40, 107-113.
23. Ohta, T., Ina, Y., 1995. Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences. J. Mol. Evol. 41, 717-720.
24. Pesole, G., Dellisanti, G., Preparata, G., Sacconne, C., 1995. The importance of base composition in the correct assessment of genetic distance. J. Mol. Evol. 41, 1124-1127.
25. Robinson, M., Gautier, C., Mouchiroud, D., 1997. Evolution of isochores in rodents. Mol. Biol. Evol. 14, 823-828.
26. Sabeur, G., Macaya, G., Kadi, F., Bernardi, G., 1993. The isochore patterns of mammalian genomes and their phylogenetic implications. J. Mol. Evol. 37, 93-108.
27. Saccone, C., Lanave, C., Pesole, G., 1993. Time and biosequences. J. Mol. Evol. 37, 154-159.
28. Saccone, C., Pesole, G., Preparata, G., 1989. DNA microenvironments and the molecular clock. J. Mol. Evol. 29, 407-411.
29. Salinas, J., Zerial, M., Filipski, J., Bernardi, G., 1986. Gene distribution and nucleotide sequence organization in the mouse genome. Eur. J. Biochem. 16, 469-485.
30. Steel, M.A., Lockhart, P.J., Penny, D., 1993. Confidence in evolutionary trees from biological sequence data. Nature 364, 440-442.
31. Zoubak, S., D'Onofrio, G., Cacciò, S., Bernardi, G., Bernardi, G., 1995. Specific compositional patterns of synonymous positions in homologous mammalian genes. J. Mol. Evol. 40, 293-307.
32. Wu, C.-I, Li, W.H., 1985. Evidence for higher rates of nucleotide substitution in rodents than in human. Proc. Natl. Acad. Sci. USA 82, 1741-1745.