Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

BMC Biology

Volumn 4, Issue , 2006, Pages

  Singh, Nadia D ^a   Arndt, Peter F ^b   Petrov, Dmitri A ^a  

^a STANFORD UNIVERSITY   (United States)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GENOMIC DNA; GUANINE; CODON; DROSOPHILA PROTEIN;

ARTICLE; CODON; CONTROLLED STUDY; DNA CONTENT; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA SALTANS; DROSOPHILA WILLISTONI; GENE MUTATION; GENETIC DIFFERENCE; GENOME; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; QUANTITATIVE ANALYSIS; RETROPOSON; SPECIES DIFFERENCE; SUBSTITUTION LINE; ANIMAL; CLASSIFICATION; DNA BASE COMPOSITION; GC RICH SEQUENCE; GENETICS; METABOLISM; MUTAGENESIS; PHYLOGENY;

DROSOPHILA MELANOGASTER; DROSOPHILA SALTANS;

ANIMALS; BASE COMPOSITION; CODON; DROSOPHILA; DROSOPHILA PROTEINS; GC RICH SEQUENCE; GENOME; MUTAGENESIS; PHYLOGENY; SPECIES SPECIFICITY;

EID: 33750622610     PISSN: 17417007     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-4-37     Document Type: Article

References (45)

1. Shields DC, Sharp PM, Higgins DG, Wright F: 'Silent' sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molec Biol Evol 1988, 5:704-716.
2. Akashi H, Kliman RM, Eyre-Walker A: Mutation pressure, natural selection, and the evolution of base composition in Drosophila. Genetica (Dordrecht) 1998, 102-103:49-60.
3. Akashi H, Eyre-Walker A: Translational selection and molecular evolution. Current Opinion in Genetics & Development 1998. 8:688-693.
4. Bulmer M: The selection-mutation-drift theory of synonymous codon usage. Genetics 1991, 129:897-908.
5. Carlini DB, Stephan W: In Vivo Introduction of Unpreferred Synonymous Codons Into the Drosophila Adh Gene Results in Reduced Levels of ADH Protein. Genetics 2003, 163:239-243.
6. Bulmer M: Are codon usage patterns in unicellular organisms determined by selection mutation balance? Journal of Evolutionary Biology 1988, 1:15-26.
7. Duret L, Mouchiroud D: Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 1999, 96:4482-4487.
8. Sharp PM, Li WH: An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution 1986, 24:28-38.
9. Comeron JM, Kreitman M, Aguade M: Natural Selection on Synonymous Sites is Correlated with Gene Length and Recombination in Drosophila. Genetics 1999, 151:239-249.
10. Akashi H: Molecular Evolution Between Drosophila melanogaster and D. simulans: Reduced Codon Bias. Faster Rates of Amino Acid Substitution, and Larger Proteins in D. melanogaster. Genetics 1996, 144:1297-1307.
11. Eyre-Walker A: Synonymous codon bias is related to gene length in coli Escherichia: Selection for translational accuracy? Molecular Biology and Evolution 1996, 13:864-872.
12. Marais G, Duret L: Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. Journal of Molecular Evolution 2001, 52:275-280.
13. Marais G, Mouchiroud D, Duret L: Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proceedings of the National Academy of Sciences of the United States of America 2001, 98:5688-5692.
14. Marais G, Mouchiroud D, Duret L: Neutral effect of recombination on base composition in Drosophila. Genetical Research 2003, 81:79-87.
15. Singh ND, Arndt PF, Petrov DA: Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster. Genetics 2004, 169:709-722.
16. Hey J, Kliman RM: Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 2002, 160:595-608.
17. Kliman RM, Hey J: Reduced natural selection associated with low recombination in Drosophila melanogaster. Molecular Biology and Evolution 1993, 10:1239-1258.
18. Marais G, Piganeau G: Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes. Molecular Biology and Evolution 2002, 19:1399-1406.
19. Grantham R, Gautier C, Gouy M, Mercier R, Pave A: Codon catalog usage and the genome hypothesis. Nucliec Acids Research 1980, 8:r49-r62.
20. Powell JR, DeSalle R: Drosophila Molecular Phylogenies and Their Uses. Evolutionary Biology 1995, 28:87-138.
21. Akashi H, Schaeffer SW: Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 1997, 146:295-307.
22. Rodriguez-Trelles F, Tarrio R, Ayala FJ: Evidence for a high ancestral GC content in Drosophila. Molecular Biology and Evolution 2000, 17:1710-1717.
23. Rodriguez-Trelles F, Tarrio R, Ayala FJ: Switch in codon bias and increased rates of amino acid substitution in the Drosophila, saltans species group. Genetics 1999, 153:339-350.
24. Anderson CL, Carew EA, Powell JR: Evolution of the Adh locus in the Drosophila willistoni group: The loss of an intron, and shift in codon usage. Molecular Biology and Evolution 1993, 10:605-618.
25. Rodriguez-Trelles F, Tarrio R, Ayala FJ: Fluctuating mutation bias and the evolution of base composition in Drosophila. Journal of Molecular Evolution 2000, 50:1-10.
26. Rodriguez-Trelles F, Tarrio R, Ayala FJ: Molecular evolution and phylogeny of the Drosophila saltans species group inferred from the Xdh gene. Molecular Phylogenetics and Evolution 1999, 13:110-121.
27. Powell JR, Sezzi E, Moriyama EN, Gleason JM, Caccone A: Analysis of a shift in codon usage in Drosophila. Journal of Molecular Evolution 2003, 57:S214-S225.
28. Rodriguez-Trelles F, Tarrio R, Ayala FJ: Disparate evolution of paralagous introns in the Xdh gene of Drosophlia. Journal of Molecular Evolution 2000, 50:123-130.
29. Besansky NJ, Bedell JA, Mukabayire O: Q: A new retrotransposon from the mosquito Anopheles gamblae. Insect Molecular Biology 1994, 3:49-56.
30. Petrov DA, Lozovskaya ER, Hartl DL: High intrinsic rate of DNA loss in Drosophila. Nature (London) 1996, 384:346-349.
31. Luan DD, Korman MH, Jakubczak JL, Eickbush TH: Reverse transcription R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 1993, 72:595-605.
32. Petrov DA, Hard DL: Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proceedings of the National Academy of Sciences of the United States of America 1999, 96:1475-1479.
33. Lipatov M, Arndt PF, Hwa T, Petrov DA: A Novel Method Distinguishes Between Mutation Rates and Fixation Biases in Patterns of Single-Nucleotide Substitution. Journal of Molecular Evolution 2000, 62:168-175.
34. Neafsey DE, Palumbi SR: Genome Size Evolution in Pufferfish: A Comparative Analysis of Diodontid and Tetraodontid Pufferfish Genomes. Genome Research 2003, 13:821-830.
35. Arndt PF, Petrov DA, Hwa T: Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Molecular Biology and Evolution 2003, 20:1887-1896.
36. Arndt PF, Hwa T: Identification and Measurement of Neighbor Dependent Nucleotide Substitution Processes. Bioinformatics 2005, 21:2322-2328.
37. Singh ND, Petrov DA: Rapid sequence turnover at an intergenic locus in Drosophila. Molec Biol Evol 2004, 21:670-80.
38. Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P: Patterns of intron sequence evolution in Drosophlia are dependent on length and GC content. Genome Research 2005, 6:R67.
39. Aguilera A: The connection between transcription and genomic instability. EMBO (European Molecular Biology Organization) Journal 2002, 21:195-201.
40. Akashi H, Ko WY, Plao SF, John A, Goel P, Lin CF, Vitins AP: Molecular evolution in the Drosophila melanogaster species sub-group: Frequent parameter fluctuations on the timescale of molecular divergence. Genetics 2006, 172:1711-1726.
41. DuMont VB, Fay JC, Calabrese PP, Aquadro CF: DNA variability and divergence at the Notch locus in Drosophila melanogaster and D. simulans: A case of accelerated synonymous site divergence. Genetics 2004, 167:171-185.
42. Tarrio R, Rodriguez-Trelles F, Ayala FJ: New Drosophila Introns originate by duplication. Proc Natl Acad Sci U S A 1998, 93:1658-1662.
43. Wright DA, Ke N, Smalle J, Hauge BM, Goodman HM, Voytas DF: Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana. Genetics 1996, 142:1569-578.
44. Arndt PF, Burge CB, Hwa T: DNA Sequence Evolution with Neighbor-Dependent Mutation. Journal of Computational Biology 2003, 10:313-322.
45. Petrov DA, Hartl DL: High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Molecular Biology and Evolution 1998, 15:293-302.