Constraint and turnover in sex-biased gene expression in the genus Drosophila

Nature

Volumn 450, Issue 7167, 2007, Pages 233-237

  Zhang, Yu ^a   Sturgill, David ^a   Parisi, Michael ^a,c   Kumar, Sudhir ^b   Oliver, Brian ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b Arizona State University   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARRAY; COMPARATIVE STUDY; EVOLUTION; FLY; GENE EXPRESSION; PHENOTYPE; PLEIOTROPY; SEX-RELATED DIFFERENCE;

ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; DNA SEQUENCE; DROSOPHILA; EVOLUTIONARY ADAPTATION; FEMALE; GENE EXPRESSION; GENE SEQUENCE; GENETIC TRAIT; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENITAL SYSTEM; GENOME; GONAD; MALE; NONHUMAN; PHENOTYPE; PLEIOTROPY; PRIORITY JOURNAL; SEX DIFFERENCE; SPERM; TURNOVER TIME;

DROSOPHILA ANANASSAE; DROSOPHILA MELANOGASTER; DROSOPHILA MOJAVENSIS; DROSOPHILA PSEUDOOBSCURA; DROSOPHILA SIMULANS; DROSOPHILA VIRILIS; DROSOPHILA YAKUBA;

EID: 36049041622     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature06323     Document Type: Article

References (40)

1. Denver, D. R. et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature Genet. 37, 544-548 (2005).
2. Jordan, I. K., Marino-Ramirez, L. & Koonin, E. V. Evolutionary significance of gene expression divergence. Gene 345, 119-126 (2005).
3. Khaitovich, P., Enard, W., Lachmann, M. & Paabo, S. Evolution of primate gene expression. Nature Rev. Genet. 7, 693-702 (2006).
4. Rifkin, S. A., Houle, D., Kim, J. & White, K. P. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature 438, 220-223 (2005).
5. Rifkin, S. A., Kim, J. & White, K. P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nature Genet. 33, 138-144 (2003).
6. Powell, J. R. Progress and Prospects in Evolutionary Biology: The Drosophila Model (Oxford Univ. Press, Oxford, 1997).
7. Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
8. Richards, S. et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15, 1-18 (2005).
9. Drosophila 12 Genomes Consortium. Evolution of genes and genomes in the Drosophila phylogeny. Nature doi:10.1038/nature06341 (this issue).
10. Ellegren, H. & Parsch, J. The evolution of sex-biased genes and sex-biased gene expression. Nature Rev. Genet. 8, 689-698 (2007).
11. Tamura, K., Subramanian, S. & Kumar, S. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 21, 36-44 (2004).
12. Nuzhdin, S. V., Wayne, M. L., Harmon, K. L. & McIntyre, L. M. Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol. Biol. Evol. 21, 1308-1317 (2004).
13. Ranz, J. M., Castillo-Davis, C. I., Meiklejohn, C. D. & Hartl, D. L. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300, 1742-1745 (2003).
14. Harris, M. A. et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261 (2004).
15. Ohta, T. & Gillespie, J. H. Development of neutral and nearly neutral theories. Theor. Popul. Biol. 49, 128-142 (1996).
16. Hsieh, W. P., Chu, T. M., Wolfinger, R. D. & Gibson, G. Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics 165, 747-757 (2003).
17. Khaitovich, P., Paabo, S. & Weiss, G. Toward a neutral evolutionary model of gene expression. Genetics 170, 929-939 (2005).
18. Lemos, B., Meiklejohn, C. D., Caceres, M. & Hartl, D. L. Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories. Evolution Int. J. Org. Evolution 59, 126-137 (2005).
19. Wray, G. A. The evolutionary significance of cis-regulatory mutations. Nature Rev. Genet. 8, 206-216 (2007).
20. Li, W. H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36, 96-99 (1993).
21. Khaitovich, P. et al. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309, 1850-1854 (2005).
22. Subramanian, S. & Kumar, S. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168, 373-381 (2004).
23. Miller, G. T. & Pitnick, S. Sperm-female coevolution in Drosophila. Science 298, 1230-1233 (2002).
24. FitzGerald, P. C., Sturgill, D., Shyakhtenko, A., Oliver, B. & Vinson, C. Comparative genomics of Drosophila and human core promoters. Genome Biol. 7, R53 (2006).
25. Schmidt, E. E. & Schibler, U. High accumulation of components of the RNA polymerase II transcription machinery in rodent spermatids. Development 121, 2373-2383 (1995).
26. Struhl, K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nature Struct. Mol. Biol. 14, 103-105 (2007).
27. Perrimon, N., Mohler, D., Engstrom, L. & Mahowald, A. P. X-linked female-sterile loci in Drosophila melanogaster. Genetics 113, 695-712 (1986).
28. Parisi, M. et al. A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol. 5, R40 (2004).
29. Singh, S. R., Singh, B. N. & Hoenigsberg, H. F. Female remating, sperm competition and sexual selection in Drosophila. Genet. Mol. Res. 1, 178-215 (2002).
30. Parra, G., Blanco, E. & Guigo, R. GeneID in Drosophila. Genome Res. 10, 511-515 (2000).
31. Grumbling, G. & Strelets, V. FlyBase: anatomical data, images and queries. Nucleic Acids Res. 34, D484-D488 (2006).
32. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Wheeler, D. L. GenBank. Nucleic Acids Res. 34, D16-D20 (2006).
33. Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
34. Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A. & Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 (Suppl 1), S96-S104 (2002).
35. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B. Methodological 57, 289-300 (1995).
36. Charif, D. & Lobry, J. R. in Structural approaches to sequence evolution: Molecules, networks, populations (eds Bastolla, U. M.P., Roman, H. E. and Vendruscolo, M.) (2006).
37. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. Evol. 24, 1596-1599 (2007).
38. de Hoon, M. J., Imoto, S., Nolan, J. & Miyano, S. Open source clustering software. Bioinformatics 20, 1453-1454 (2004).
39. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
40. Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).