Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome

Journal of Molecular Evolution

Volumn 61, Issue 3, 2005, Pages 315-324

  Singh, Nadia D ^a   Davis, Jerel C ^a   Petrov, Dmitri A ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Codon bias; Drosophila; Recombination

Indexed keywords

ARTICLE; AUTOSOME; CODON USAGE; CORRELATION ANALYSIS; DROSOPHILA MELANOGASTER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC RECOMBINATION; HEMIZYGOSITY; MOLECULAR EVOLUTION; SEX DETERMINATION; SEX DIFFERENCE; X CHROMOSOME;

ANIMALS; BASE COMPOSITION; BIAS (EPIDEMIOLOGY); CODON; DROSOPHILA MELANOGASTER; OPEN READING FRAMES; RECOMBINATION, GENETIC; X CHROMOSOME;

DROSOPHILA MELANOGASTER;

EID: 25144452814     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0287-1     Document Type: Article

References (51)

1. Akashi H (1994) Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy. Genetics 136:927-935
2. Akashi H (1995) Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139:1067-1076
3. Akashi H (1996) Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias. Faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144:1297-1307
4. Akashi H, Eyre-Walker A (1998) Translational selection and molecular evolution. Curr Opin Genet Dev 8:688-693
5. Akashi H, Kliman RM, Eyre-Walker A (1998) Mutation pressure, natural selection, and the evolution of base composition in Drosophila. Genetica (Dordrecht) 102-103:49-60
6. Aquadro CF (1997) Insights into the evolutionary process from patterns of DNA sequence variability. Curr Opin Genet Dev 7:835-840
7. Begun DJ, Aquadro CF (1992) Levels of naturally occurring DNA polymorphism correlate with recombination rates in Drosophila melanogaster. Nature (London) 356:519-520
8. Betancourt AJ, Presgraves DC (2002) Linkage limits the power of natural selection in Drosophila. Proc Natl Acad Sci USA 99:13616-13620
9. Betran E, Thornton K, Long M (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12:1854-1859
10. Birdsell JA (2002) Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol 19:1181-1197
11. Bridges CB (1935) Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. J Hered 26:60-64
12. Bulmer M (1988) Are codon usage patterns in unicellular organisms determined by selection mutation balance? J Evol Biol 1:15-26
13. Bulmer M (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-908
14. Caballero A (1995) On the effective size of populations with separate sexes, with particular reference to sex-linked genes. Genetics 139:1007-1011
15. Carvalho AB, Clark AG (1999) Intron size and natural selection. Nature (London) 401:344
16. Charlesworth B (1991) The evolution of sex chromosomes. Science (Washington DC) 251:1030-1033
17. Charlesworth B, Coyne JA, Barton NH (1987) The relative rates of evolution of sex chromosomes and autosomes. Am Natural 130:113-146
18. Comeron JM, Kreitman M (1998) The correlation between synonymous and nonsynonymous substitutions in Drosophila: Mutation, selection or relaxed constraints? Genetics 150:767-775
19. Comeron JM, Kreitman M (2000) The correlation between intron length and recombination in Drosophila: Dynamic equilibrium between mutational and selective forces. Genetics 156:1175-1190
20. Comeron JM, Kreitman M (2002) Population, evolutionary and genomic consequences of interference selection. Genetics 161:389-410
21. Comeron JM, Kreitman M, Aguade M (1999) Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151:239-249
22. Conery JS, Lynch M (2001) Nucleotide substitutions and the evolution of duplicate genes. Pacific Symposium on Biocomputing, pp 167-178
23. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA 96:4482-4487
24. Duret L, Mouchiroud D (2000) Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate. Mol Biol Evol 17:68-74
25. Emerson JJ, Kaessmann H, Betran E, Long M (2004) Extensive gene traffic on the mammalian X chromosome. Science (Washington DC) 303:537-540
26. Eyre-Walker A (1996) Synonymous codon bias is related to gene length in Escherichia coli: Selection for translational accuracy? Mol Biol Evol 13:864-872
27. Hey J, Kliman RM (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160:595-608
28. Hill WG, Robertson A (1966) The effect of linkage on limits to artificial selection. Genet Res 8:269-294
29. Kim Y (2004) Effect of strong directional selection on weakly selected mutations at linked sites: Implication for synonymous codon usage. Mol Biol Evol 21:286-294
30. Kindahl EC (1994) Recombination and DNA polymorphism on the third chromosome of Drosophila melanogaster. Cornell University, Ithaca, NY
31. Kliman RM, Hey J (1993) Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol Biol Evol 10:1239-1258
32. Kliman RM, Hey J (2003) Hill-Robertson interference in Drosophila melanogaster: Reply to Marais, Mouchiroud and Duret. Genet Res 81:89-90
33. Krylov DM, Wolf YI, Rogozin IB, Koonin EV (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 13:2229-2235
34. Langley CH, Lazzaro BP, Phillips W, Heikkinen E, Braverman JM (2000) Linkage disequilibria and the site frequency spectra in the su(s) and su(wa) regions of the Drosophila melanogaster X chromosome. Genetics 156:1837-1852
35. Laporte V, Charlesworth B (2002) Effective population size and population subdivision in demographically structured populations. Genetics 162:501-519
36. Marais G, Duret L (2001) Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J Mol Evol 52:275-280
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 USA 98:5688-5692
38. Marais G, Mouchiroud D, Duret L (2003) Neutral effect of recombination on base composition in Drosophila. Genet Res 81:79-87
39. Marin I, Siegal ML, Baker BS (2000) The evolution of dosage-compensation mechanisms. Bioessays 22:1106-1114
40. Pal C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158:927-931
41. Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B (2003) Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science (Washington DC) 299:697-700
42. Schmid KJ, Aquadro CF (2001) The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes. Genetics 159:589-598
43. Sharp PM, Li WH (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24:28-38
44. Shields DC, Sharp PM, Higgins DG, Wright F (1988) 'Silent' sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol 5:704-716
45. Singh ND, Arndt PF, Petrov DA (2005) Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics 169:709-722
46. Sorsa V (1988) Chromosome maps of Drosophila. CRC Press, Boca Raton, FL
47. Subramanian S, Kumar S (2004) Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381
48. Takano-Shimizu T (1999) Local recombination and mutation effects on molecular evolution in Drosophila. Genetics 153:1285-1296
49. True JR, Mercer JM, Laurie CC (1996) Differences in crossover frequency and distribution among three sibling species of Drosophila. Genetics 142:507-523
50. Wright SI, Yau CBK, Looseley M, Meyers BC (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol 21:1719-1726
51. Yang Z (1997) PAML: am program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556