Retroposed new genes out of the X in Drosophila

Genome Research

Volumn 12, Issue 12, 2002, Pages 1854-1859

  Betrán, Esther ^a   Thornton, Kevin ^a   Long, Manyuan ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOSOME; CHROMOSOME SUBSTITUTION; DROSOPHILA MELANOGASTER; EVOLUTION; GENE EXPRESSION; GENE FUNCTION; GENETICS; GENOME; NATURAL SELECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW; SPERMATOGENESIS; TESTIS; X CHROMOSOME; X CHROMOSOME INACTIVATION;

ANIMALS; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; GENES, INSECT; MOLECULAR SEQUENCE DATA; RETROELEMENTS; X CHROMOSOME;

DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0036906987     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.6049     Document Type: Review

References (42)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Andrews, J., Bouffard, G.G., Cheadle, C., Lu, J., Becker, K.G., and Oliver, B. 2000. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res. 10: 2030-2043.
3. Ashburner, M. 1989. Drosophila: A laboratory handbook. Cold Spring Harbor Laboratory Press, New York.
4. Begun, D.J. 1997. Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics 145: 375-382.
5. Bownes, M. 1990. Preferential insertion of P elements into genes expressed in the germ-line of Drosophila melanogaster. Mol. Gen. Genet. 222: 457-460.
6. Brosius, J. 1991. Retroposons-Seeds of evolution. Science 251: 753.
7. Brosius, J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115-134.
8. Castrillon, D.H., Gonczy, P., Alexander, S., Rawson, R., Eberhart, C.G., Viswanathan, S., DiNardo, S., and Wasserman, S.A. 1993. Toward a molecular genetic analysis of spermatogenesis in Drosophila melanogaster: Characterization of male-sterile mutants generated by single P element mutagenesis. Genetics 135(2):489-505.
9. Charlesworth, B., Coyne, J.A., and Barton, N.H. 1987. The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 130: 113-146.
10. Comeron, J.M. 1999. K-Estimator: Calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 15: 763-764.
11. Dahl, H-H.M., Brown, R. M., Hutchison, W.M., Maragos, C., and Brown, G.K. 1990. A testis-specific form of the human pyruvate dehydrogenase E1 α subunit is coded for by an intronless gene on chromosome 4. Genomics 8: 225-232.
12. Eddy, E.M. and O'Brien, D.A. 1998. Gene expression during mammalian meiosis. Curr. Top. Dev. Biol. 37: 141-199.
13. Gilbert, W. 1978. Why genes in pieces? Nature 217: 501.
14. Gonçalves, I., Duret, L., and Mouchiroud, D. 2000. Nature and structure of human genes that generate retropseudogenes. Genome Res. 10: 672-678.
15. Hurst, L.D. and Randerson, J.P. 1999. An eXceptional chromosome. Trends Genet. 15: 383-385.
16. Lander, E.S., Linton, L.M., Birren B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
17. Langley, C.H., Montgomery, E., Hudson, R., Kaplan, N., and Charlesworth, B. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet. Res. 52: 223-235.
18. Lemeunier, F. and Ashburner, M. 1976. Relationships in the melanogaster species subgroup of the genus Drosophila (Sophophora). II. Phylogenetic relationships between six species based upon polytene banding sequences. Proc. R. Soc. Lond. B. 193: 257-294.
19. Li, W-H. 1997. Molecular evolution. Sinauer Associates Sunderland, MA.
20. Lifschytz, E. and Lindsley, D.L. 1972. The role of X-chromosome inactivation during spermatogenesis. Proc. Nat. Acad. Sci. 69: 182-186.
21. Long, M. 2001. Evolution of novel genes. Curr. Opin. Genet. Dev. 11: 673-680.
22. Long, M. and Langley, C. H. 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.
23. Long, M., Wang, W., and Zhang, J. 1999. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 238: 135-141.
24. McCarrey, J.R. 1994. Evolution of tissue-specific gene expression in mammals. How a new phosphoglycerate kinase was formed and refined. Bioscience 44: 20-27.
25. McCarrey, J.R. and Thomas, K. 1987. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326: 501-505.
26. Nurminsky, D.I., Nurminskaya, M.V., Aguilar, D.D., and Hartl, D.L. 1998. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575.
27. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, New York, NY.
28. Pasyukova, E., Nuzhdin, S., Li, W., and Flavell, A.J. 1997. Germ line transposition of the copia retrotransposon in Drosophila melanogaster is restricted to males by tissue-specific control of copia RNA levels. Mol. Gen. Genet. 255: 115-124.
29. Pearson, W.R. 1990. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183: 63-98.
30. Petrov, D.A., Sangster, T.A., Johnston, J.S., Hartl, D.L., and Shaw, K.L. 2000. Evidence for DNA loss as a determinant of genome size. Science 287: 1060-1062.
31. Powell, J.R. 1997. Progress and prospects in evolutionary biology: The Drosophila model, p. 355, Oxford University Press, New York, NY.
32. Reinke, V., Smith, H.E., Nance, J., Wang, J., Van Doren, C., Begley, R., Jones, S.J.M., Davis, E.B., Scherer, S., Ward, S., et al. 2000. A global profile of germline gene expression in C. elegans. Mol. Cell 6: 605-616.
33. Rice, W.R. 1984. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38: 735-742.
34. Richler, C., Soreq, H., and Wahrman, J. 1992. X inactivation in mammalian testis is correlated with inactive X-specific transcription. Nat. Genet. 2: 192-195.
35. Rozas, J. and Rozas, R. 1999. DnaSP version 3.52: An integrated program for molecular population genetics and molecular evolution. Bioinformatics 15: 174-175.
36. Thornton, K. and Long, M. 2002. Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Mol. Biol. Evol. 19: 918-925.
37. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
38. Wang, P.J., McCarrey, J.R., Yang, F. and Page, D.C. 2001. An abundance of X-linked genes expressed in spermatogonia. Nat. Genet. 27: 422-426.
39. Wang, W., Zhang, J., Alvarez, C., Llopart, A., and Long, M. 2000. The origin of the jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Mol. Biol. Evol. 17: 1294-1301.
40. Wang, W., Brunet, F.G., Nevo, E., and Long, M. 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Nat. Acad. Sci. 99: 4448-4453
41. Watterson, G.A. 1983. On the time for gene silencing at duplicate loci. Genetics 105: 745-766.
42. Yang, Z. 1998. Likelihood ratio test for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15: 568-573.