Strong regional biases in nucleotide substitution in the chicken genome

Molecular Biology and Evolution

Volumn 23, Issue 6, 2006, Pages 1203-1216

  Webster, Matthew T ^a,b   Axelsson, Erik ^a   Ellegren, Hans ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

Base composition; Chicken; Isochore; Mutation; Recombination

Indexed keywords

NUCLEOTIDE;

ANALYSIS OF VARIANCE; ANALYTIC METHOD; ANIMAL CELL; ANIMAL GENETICS; ARTICLE; AUTOSOME; CHICKEN; CHROMOSOME SUBSTITUTION; COMPARATIVE STUDY; CONTROLLED STUDY; EVOLUTION; FREQUENCY ANALYSIS; GENE CONVERSION; GENE FREQUENCY; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME; ISOCHORE; MICROCHROMOSOME; MODEL; MUTATION; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; QUAIL; REINFORCEMENT; TURKEY (BIRD);

ALU ELEMENTS; ANIMALS; BASE COMPOSITION; CHICKENS; COTURNIX; CPG ISLANDS; EVOLUTION, MOLECULAR; GENE CONVERSION; GENOME; HUMANS; INTRONS; LIKELIHOOD FUNCTIONS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; POINT MUTATION; TURKEYS;

ANIMALIA; AVES; MAMMALIA; MELEAGRIS GALLOPAVO; PHASIANIDAE;

EID: 33646884615     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msk008     Document Type: Article

References (75)

1. Alvarez-Valin, F., O. Clay, S. Cruveiller, and G. Bernardi. 2004. Inaccurate reconstruction of ancestral GC levels creates a "vanishing isochores" effect. Mol. Phylogenet. Evol. 31:788-793.
2. Antezana, M. A. 2005. Mammalian GC content is very close to mutational equilibrium. J. Mol. Evol. 61:834-836.
3. Arndt, P. F., C. B. Burge, and T. Hwa. 2003. DNA sequence evolution with neighbor-dependent mutation. J. Comput. Biol. 10:313-322.
4. Arndt, P. F., T. Hwa, and D. A. Petrov. 2005. Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J. Mol. Evol. 60:748-763.
5. Arndt, P. F., D. A. Petrov, and T. Hwa. 2003. Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Mol. Biol. Evol. 20:1887-1896.
6. Axelsson, E., M. T. Webster, N. G. Smith, D. W. Burt, and H. Ellegren. 2005. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res. 15:120-125.
7. Bao, Z., and S. R. Eddy. 2002. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12:1269-1276.
8. Belle, E. M., L. Duret, N. Galtier, and A. Eyre-Walker. 2004. The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J. Mol. Evol. 58:653-660.
9. Bernardi, G. 2000. Isochores and the evolutionary genomics of vertebrates. Gene 241:3-17.
10. Bernardi, G., S. Hughes, and D. Mouchiroud. 1997. The major compositional transitions in the vertebrate genome. J. Mol. Evol. 44(Suppl. 1):S44-S51.
11. Bernardi, G., B. Olofsson, J. Filipski, M. Zerial, J. Salinas, G. Cuny, M. Meunier-Rotival, and F. Rodier. 1985. The mosaic genome of warm-blooded vertebrates. Science 228:953-958.
12. Birdsell, J. A. 2002. Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol. Biol. Evol. 19:1181-1197.
13. Bourque, G., E. M. Zdobnov, P. Bork, P. A. Pevzner, and G. Tesler. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15:98-110.
14. Burt, D. W. 2002. Origin and evolution of avian microchromosomes. Cytogenet. Genome Res. 96:97-112.
15. Burt, D. W., C. Bruley, I. C. Dunn et al. (13 co-authors). 1999. The dynamics of chromosome evolution in birds and mammals. Nature 402:411-413.
16. Bush, G. L., S. M. Case, A. C. Wilson, and J. L. Patton. 1977. Rapid speciation and chromosomal evolution in mammals. Proc. Natl. Acad. Sci. USA 74:3942-3946.
17. Caron, H., B. van Schaik, M. van der Mee et al. (13 co-authors). 2001. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291:1289-1292.
18. Cordaux, R., D. J. Hedges, M. A. Batzer, P. L. Deininger, J. V. Moran, and H. H. Kazazian Jr. 2004. Retrotransposition of Alu elements: how many sources? Trends Genet. 20:464-467.
19. Dimcheff, D. E., S. V. Drovetski, and D. P. Mindell. 2002. Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes. Mol. Phylogenet. Evol. 24:203-215.
20. Duret, L. 2006. The GC content of primates and rodents genomes is not at equilibrium: a reply to Antezana. J. Mol. Evol. (in press).
21. Duret, L., M. Semon, G. Piganeau, D. Mouchiroud, and N. Galtier. 2002. Vanishing GC-rich isochores in mammalian genomes. Genetics 162:1837-1847.
22. Ellegren, H., N. G. Smith, and M. T. Webster. 2003. Mutation rate variation in the mammalian genome. Curr. Opin. Genet. Dev. 13:562-568.
23. Eyre-Walker, A. 1993. Recombination and mammalian genome evolution. Proc. R. Soc. Lond. B Biol. Sci. 252:237-243.
24. _. 1998. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47:686-690.
25. Filatov, D. A. 2004. A gradient of silent substitution rate in the human pseudoautosomal region. Mol. Biol. Evol. 21: 410-417.
26. 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.
27. Filipski, J., J. P. Thiery, and G. Bernardi. 1973. An analysis of the bovine genome by Cs2SO4-Ag density gradient centrifugation. J. Mol. Biol. 80:177-197.
28. Fullerton, S. M., A. Bernardo Carvalho, and A. G. Clark. 2001. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18:1139-1142.
29. Galtier, N. 2003. Gene conversion drives GC content evolution in mammalian histones. Trends Genet. 19:65-68.
30. Galtier, N., G. Piganeau, D. Mouchiroud, and L. Duret. 2001. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159:907-911.
31. Gregory, T. R. 2005. Animal genome size database. (http://www.genomesize. com).
32. Hedges, S. B., and L. L. Poling. 1999. A molecular phylogeny of reptiles. Science 283:998-1001.
33. Hellmann, I., I. Ebersberger, S. E. Ptak, S. Paabo, and M. Przeworski. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72:1527-1535.
34. Hughes, S., O. Clay, and G. Bernardi. 2002. Compositional patterns in reptilian genomes. Gene 295:323-329.
35. Hughes, S., D. Zelus, and D. Mouchiroud. 1999. Warm-blooded isochore structure in Nile crocodile and turtle. Mol. Biol. Evol. 16:1521-1527.
36. Hurst, L. D., C. F. Brunton, and N. G. Smith. 1999. Small introns tend to occur in GC-rich regions in some but not all vertebrates. Trends Genet. 15:437-439.
37. Hurst, L. D., and E. J. Williams. 2000. Covariation of GC content and the silent site substitution rate in rodents: implications for methodology and for the evolution of isochores. Gene 261:107-114.
38. [ICGSC] International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
39. [IHGSC] International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
40. Jaillon, O., J. M. Aury, F. Brunet et al. (61 co-authors). 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.
41. Jurka, J. 2000. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16:418-420.
42. Kapitonov, V., and J. Jurka. 1996. The age of Alu subfamilies. J. Mol. Evol. 42:59-65.
43. Kauppi, L., A. J. Jeffreys, and S. Keeney. 2004. Where the crossovers are: recombination distributions in mammals. Nat. Rev. Genet. 5:413-424.
44. Kong, A., D. F. Gudbjartsson, J. Sainz et al. (16 co-authors). 2002. A high-resolution recombination map of the human genome. Nat. Genet. 31:241-247.
45. Lercher, M. J., and L. D. Hurst. 2002. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:337-340.
46. Lercher, M. J., N. G. Smith, A. Eyre-Walker, and L. D. Hurst. 2002. The evolution of isochores. Evidence from SNP frequency distributions. Genetics 162:1805-1810.
47. Lercher, M. J., A. O. Urrutia, A. Pavlicek, and L. D. Hurst. 2003. A unification of mosaic structures in the human genome. Hum. Mol. Genet. 12:2411-2415.
48. Marais, G. 2003. Biased gene conversion: implications for genome and sex evolution. Trends Genet. 19:330-338.
49. McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
50. McVean, G. A., S. R. Myers, S. Hunt, P. Deloukas, D. R. Bentley, and P. Donnelly. 2004. The fine-scale structure of recombination rate variation in the human genome. Science 304:581-584.
51. Meunier, J., and L. Duret. 2004. Recombination drives the evolution of GC-content in the human genome. Mol. Biol. Evol. 21:984-990.
52. Meunier, J., A. Khelifi, V. Navratil, and L. Duret. 2005. Homology-dependent methylation in primate repetitive DNA. Proc. Natl. Acad. Sci. USA 102:5471-5476.
53. Montoya-Burgos, J. I., P. Boursot, and N. Galtier. 2003. Recombination explains isochores in mammalian genomes. Trends Genet. 19:128-130.
54. Mouchiroud, D., G. D'Onofrio, B. Aissani, G. Macaya, C. Gautier, and G. Bernardi. 1991. The distribution of genes in the human genome. Gene 100:181-187.
55. Nagylaki, T. 1983. Evolution of a finite population under gene conversion. Proc. Natl. Acad. Sci. USA 80:6278-6281.
56. Nekrutenko, A., and W. H. Li. 2000. Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 10:1986-1995.
57. Otto, S. P., and T. Lenormand. 2002. Resolving the paradox of sex and recombination. Nat. Rev. Genet. 3:252-261.
58. Pardo-Manuel de Villena, F., and C. Sapienza. 2001. Female meiosis drives karyotypic evolution in mammals. Genetics 159:1179-1189.
59. Piganeau, G., D. Mouchiroud, L. Duret, and C. Gautier. 2002. Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores. J. Mol. Evol. 54:129-133.
60. Ptak, S. E., A. D. Roeder, M. Stephens, Y. Gilad, S. Paabo, and M. Przeworski. 2004. Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol. 2:e155.
61. Saccone, S., A. De Sario, J. Wiegant, A. K. Raap, G. Della Valle, and G. Bernardi. 1993. Correlations between isochores and chromosomal bands in the human genome. Proc. Natl. Acad. Sci. USA 90:11929-11933.
62. Shetty, S., D. K. Griffin, and J. A. Graves. 1999. Comparative painting reveals strong chromosome homology over 80 million years of bird evolution. Chromosome Res. 7:289-295.
63. Smith, N. G., and A. Eyre-Walker. 2002. The compositional evolution of the murid genome. J. Mol. Evol. 55:197-201.
64. Smith, N. G., M. T. Webster, and H. Ellegren. 2002. Deterministic mutation rate variation in the human genome. Genome Res. 12:1350-1356.
65. Sueoka, N. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85:2653-2657.
66. Templeton, A. R., A. G. Clark, K. M. Weiss, D. A. Nickerson, E. Boerwinkle, and C. F. Sing. 2000. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet. 66:69-83.
67. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
68. Vinogradov, A. E. 2003. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 31:1838-1844.
69. _. 2005. Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res. 33:559-563.
70. Webster, M. T., and N. G. Smith. 2004. Fixation biases affecting human SNPs. Trends Genet. 20:122-126.
71. Webster, M. T., N. G. Smith, and H. Ellegren. 2003. Compositional evolution of noncoding DNA in the human and chimpanzee genomes. Mol. Biol. Evol. 20:278-286.
72. Webster, M. T., N. G. Smith, L. Hultin-Rosenberg, P. F. Arndt, and H. Ellegren. 2005. Male-driven biased gene conversion governs the evolution of base composition in human alu repeats. Mol. Biol. Evol. 22:1468-1474.
73. Wicker, T., J. S. Robertson, S. R. Schulze et al. (11 co-authors). 2005. The repetitive landscape of the chicken genome. Genome Res. 15:126-136.
74. Wolfe, K. H., P. M. Sharp, and W. H. Li. 1989. Mutation rates differ among regions of the mammalian genome. Nature 337:283-285.
75. Yang, A. S., M. L. Gonzalgo, J. M. Zingg, R. P. Millar, J. D. Buckley, and P. A. Jones. 1996. The rate of CpG mutation in Alu repetitive elements within the p53 tumor suppressor gene in the primate germline. J. Mol. Biol. 258:240-250.