Substitution patterns are GC-biased in divergent sequences across the metazoans

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 516-527

  Capra, John A ^a   Pollard, Katherine S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Biased gene conversion; Clustered substitution; Fast evolving sequence; Fixation bias; Genome analysis

Indexed keywords

ANIMALIA; CANIS FAMILIARIS; EUKARYOTA; METAZOA; PAN;

ANIMAL; ARTICLE; DNA BASE COMPOSITION; DOG; EPIDEMIOLOGY; GENE CONVERSION; GENETICS; GENOME; HUMAN; MOLECULAR EVOLUTION; MOUSE; NUCLEOTIDE SEQUENCE; PHYLOGENY; RISK; SPECIES DIFFERENCE;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; BIAS (EPIDEMIOLOGY); DOGS; EVOLUTION, MOLECULAR; GENE CONVERSION; GENOME; HUMANS; MICE; ODDS RATIO; PHYLOGENY; SPECIES SPECIFICITY;

EID: 82255162146     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr051     Document Type: Article

References (57)

1. Berglund J, Pollard KS, Webster MT. 2009. Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 7(1):e1000026.
2. Birdsell JA. 2002. Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol. 19(7):1181-1197. (Pubitemid 34743242)
3. Blanchette M, et al. 2004. Aligning multiple genomic sequences with the threaded blockset sligner. Genome Res. 14(4):708-715. (Pubitemid 38500244)
4. Charlesworth B, Charlesworth D. 1998. Some evolutionary consequences of deleterious mutations. Genetica 102-103(1-6):3-19. (Pubitemid 28371703)
5. Clé ment Y, Arndt PF. 2011. Substitution patterns are under different influences in primates and rodents. Genome Biol Evol. 3:236-245.
6. Coop G, Przeworski M. 2006. An evolutionary view of human recombination. Nat Rev Genet. 8(1):23-34. (Pubitemid 46006047)
7. Cox A, et al. 2009. A new standard genetic map for the laboratory mouse. Genetics 182(4):1335-1344.
8. Dreszer TR, Wall GD, Haussler D, Pollard KS. 2007. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 17(10):1420-1430. (Pubitemid 47529426)
9. Duret L, Arndt PF. 2008. The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet. 4(5):e1000071.
10. Duret L, Galtier N. 2009. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet. 10(1):285-311.
11. Eyre-Walker A. 1998. Problems with parsimony in sequences of biased base composition. J Mol Evol. 47:686-690. (Pubitemid 29008771)
12. Eyre-Walker A, Hurst LD. 2001. The evolution of isochores. Nat Rev Genet. 2(7):549-555. (Pubitemid 33674028)
13. Fiston-Lavier AS, Singh ND, Lipatov M, Petrov DA. 2010. Drosophila melanogaster recombination rate calculator. Gene 463(1-2):18-20.
14. Fullerton SM, Bernardo Carvalho A, Clark AG. 2001. Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol. 18(6):1139-1142. (Pubitemid 32520487)
15. Galtier N, Duret L. 2007. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet. 23(6):273-277. (Pubitemid 46770896)
16. Galtier N, Piganeau G, Mouchiroud D, Duret L. 2001. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159(2):907-911. (Pubitemid 33035129)
17. Glémin S. 2010. Surprising fitness consequences of GC-biased gene conversion: I. Mutation load and inbreeding depression. Genetics 185(3):939-959.
18. Glémin S, Bazin E, Charlesworth D. 2006. Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proc R Soc B Biol Sci. 273(1604):3011-3019. (Pubitemid 46622432)
19. Groenen MA, et al. 2009. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 19(3):510-519.
20. Harrison RJ, Charlesworth B. 2011. Biased gene conversion affects patterns of codon usage and amino acid usage in the saccharomy-ces sensu stricto group of yeasts. Mol Biol Evol. 28(1):117-129.
21. Hernandez RD, Williamson SH, Zhu L, Bustamante CD. 2007. Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Mol Biol Evol. 24(10):2196-2202. (Pubitemid 47574720)
22. Hubisz MJ, Pollard KS, Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 12(1):41-51.
23. Hunter JD. 2007. Matplotlib: a 2D graphics environment. Comput Sci Eng. 9(3):90-95.
24. Hurst LD. 2009. Genetics and the understanding of selection. Nat Rev Genet. 10(2):83-93.
25. International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432(7018): 695-716.
26. Jackson Laboratories. 2009. Mouse map converter. [cited 2010 Mar 22]. Available from: http://cgd.jax.org/mousemapconverter/.
27. Jones E, Oliphant T, Peterson P. 2001. SciPy: Open source scientific tools for Python. [cited 2010 Oct 12]. Available from: http://www.sci-py.org/.
28. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32(Suppl 1):D493-D496. (Pubitemid 38081706)
29. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. 2010. GC-biased evolution near human accelerated regions. PLoS Genet. 6(5):e1000960.
30. Kent WJ, et al. 2003. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 100(20):11484-11489. (Pubitemid 37205962)
31. Kent WJ, et al. 2002. The Human Genome Browser at UCSC. Genome Res. 12(6):996-1006.
32. Kong A, et al. 2010. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467(7319):1099-1103.
33. Kuraku S, et al. 2006. cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Res. 14(2):187-202.
34. Lynch M, et al. 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 105(27):9272-9277.
35. Mancera E, et al. 2008. High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454(7203):479-485.
36. Marais G, Charlesworth B, Wright S. 2004. Recombination and base composition: the case of the highly self-fertilizing plant arabidopsis thaliana. Genome Biol. 5(7):R45.
37. Marais G, Mouchiroud D, Duret L. 2001. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci U S A. 98(10):5688-5692. (Pubitemid 32435703)
38. Marais G, Mouchiroud D, Duret L. 2003. Neutral effect of recombination on base composition in Drosophila. Genet Res. 81(2):79-87. (Pubitemid 36575831)
39. Meunier J, Duret L. 2004. Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol. 21(6):984-990. (Pubitemid 38658206)
40. Oliver PL, et al. 2009. Accelerated evolution of the prdm9 speciation gene across diverse metazoan taxa. PLoS Genet. 5(12):e1000753.
41. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20(1):110-121.
42. Pollard KS, Salama SR, King B, et al. 2006. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2(10):e168.
43. Pollard KS, Salama SR, Lambert N, et al. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443(7108):167-172. (Pubitemid 44387600)
44. Prabhakar S, et al. 2008. Human-specific gain of function in a developmental enhancer. Science 321(5894):1346-1350.
45. R Development Core Team. 2009. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. ISBN 3-900051-07-0
46. Ratnakumar A, et al. 2010. Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc B Biol Sci. 365(1552):2571-2580.
47. Romiguier J, Ranwez V, Douzery EJP, Galtier N. 2010. Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res. 20(8):1001-1009.
48. Sherry ST, et al. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29(1):308-311. (Pubitemid 32054478)
49. Shifman S, et al. 2006. A high-resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biol. 4(12):e395.
50. Siepel A, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15(8):1034-1050. (Pubitemid 41126859)
51. Siepel A, Haussler D. 2004. Combining phylogenetic and hidden markov models in biosequence analysis. J Comput Biol. 11(2-3): 413-428. (Pubitemid 38901670)
52. Smit A, Hubley R. 2008-2010. RepeatModeler Open-1.0. [cited 2011 Jun 16]. Available from: http://www.repeatmasker.org
53. The International Hapmap Consortium. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861.
54. Tsai IJ, Bensasson D, Burt A, Koufopanou V. 2008. Population genomics of the wild yeast Saccharomyces paradoxus: quantifying the life cycle. Proc Natl Acad Sci U S A. 105(12):4957-4962. (Pubitemid 351753853)
55. Tsai IJ, Burt A, Koufopanou V. 2010. Conservation of recombination hotspots in yeast. Proc Natl Acad Sci U S A. 107(17):7847-7852.
56. Webster MT, Axelsson E, Ellegren H. 2006. Strong regional biases in nucleotide substitution in the chicken genome. Mol Biol Evol. 23(6):1203-1216. (Pubitemid 43781595)
57. Webster MT, et al. 2005. Male-driven biased gene conversion governs the evolution of base composition in human Alu repeats. Mol Biol Evol. 22(6):1468-1474. (Pubitemid 40734197)