Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila

Genome Research

Volumn 15, Issue 10, 2005, Pages 1393-1401

  Bachtrog, Doris ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ARTICLE; CHROMOSOME DELETION; CHROMOSOME INSERTION; CHROMOSOME STRUCTURE; DNA FLANKING REGION; DROSOPHILA; EVOLUTION; FEMALE; FRAMESHIFT MUTATION; GENE SEQUENCE; INTRON; MALE; NONHUMAN; PRIORITY JOURNAL; SEX CHROMOSOME; STOP CODON; TRANSPOSON; X CHROMOSOME; Y CHROMOSOME;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA; GENE DUPLICATION; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; REGULATORY SEQUENCES, NUCLEIC ACID; SEX CHROMOSOMES; Y CHROMOSOME;

DROSOPHILA MIRANDA;

EID: 25844504316     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.3543605     Document Type: Article

References (52)

1. Akashi, H. and Schaeffer, S.W. 1997. Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 146: 295-307.
2. Andolfatto, P., Wall, J., and Kreitman, M. 1999. Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
3. Bachtrog, D. 2003a. Adaptation shapes patterns of genome evolution in sexual and asexual genomes in Drosophila. Nat. Genet. 34: 215-219.
4. _. 2003b. Accumulation of spock and worf, two novel non-LTR retrotransposons on the neo-Y chromosome of Drosophila miranda. Mol. Biol. Evol. 20: 173-181.
5. _. 2003c. Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics 165: 1221-1232.
6. _. 2004. Evidence that positive selection drives Y-chromosome degeneration in Drosophila miranda. Nat. Genet. 36: 518-522.
7. Bachtrog, D. and Charlesworth, B. 2002. Reduced adaptation of a non-recombining neo-Y chromosome. Nature 416: 323-326.
8. Bartolome, C., Maside, X., Yi, S., Grant, A., and Charlesworth, B. 2005. Patterns of selection on synonymous and nonsynonymous variants in Drosophila miranda. Genetics 169: 1495-1507.
9. Bone, J.R. and Kuroda, M.I. 1996. Dosage compensation regulatory proteins and the evolution of sex chromosomes in Drosophila. Genetics 144: 705-713.
10. Bull, J.J. 1983. Evolution of sex determining mechanisms. Benjamin Cummings, Menlo Park, CA.
11. Caceres, M., Ranz, J.M., Barbadilla, A., Long, M., and Ruiz, A. 1999. Generation of a widespread Drosophila inversion by a transposable element. Science 16: 415-418.
12. Carvalho, A.B. 2002. Origin and evolution of the Drosophila Y chromosome. Curr. Opin. Genet. Dev. 12: 664-668.
13. Carvalho, A. and Clark, A. 2005. Y Chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y. Science 307: 108-110.
14. Carvalho, A.B., Dobo, B.A., Vibranovski, M.D., and Clark, A.G. 2001. Identification of five new genes on the Y chromosome of Drosophila melanogaster. Proc. Natl. Acad. Sci. 98: 13225-13230.
15. Charlesworth, B. 1996. The evolution of chromosomal sex determination and dosage compensation. Curr. Biol. 6: 149-162.
16. Charlesworth, B. and Charlesworth, D. 2000. The degeneration of Y chromosomes. Philos. Trans. R Soc. Lond. B Biol. Sci. 355: 1563-1572.
17. Charlesworth, B. and Langley, C.H. 1989. The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23: 251-287.
18. Charlesworth, B., Sniegowski, P., and Stephan, W. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220.
19. Coghlan, A. and Wolfe, K. 2002. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 12: 857-867.
20. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium. 2000. The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100: 377-386.
21. 2 chromosome of Drosophila miranda and conservativeness in the evolution of dosage compensation. Chromosoma 87: 373-388.
22. Filatov, D. 2005. Substitution rates in a new Silene latifolia sex-linked gene, SlssX/Y. Mol. Biol. Evol. 22: 402-408.
23. Fridolfsson, A.K. and Ellegren, H. 2000. Molecular evolution of the avian CHD1 genes on the Z and W sex chromosomes. Genetics 155: 1903-1912.
24. Haddrill, P.R., Halligan, D., Charlesworth, B., and Andolfatto, P. 2005. Patterns of intron sequence evolution depend upon length and GC content. Genome Biol. 6: R67.
25. Halligan, D., Eyre-Walker, A., Andolfatto, P., and Keightley, P. 2004. Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res. 14: 273-279.
26. Jurka, J. 2000. Repbase update: A database and an electronic journal of repetitive elements. Trends Genet. 9: 418-420.
27. Kaminker, J.S., Bergman, C.M., Kronmiller, B., Carlson, J., Svirskas, R., Patel, S., Frise, E., Wheeler, D.A., Lewis, S.E., Rubin, G.M., et al. 2002. The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective. Genome Biol. 3: research0084.1-0084.20.
28. Kashkush, K., Feldman, M., and Levy, A. 2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33: 102-106.
29. Lahn, B.T., Pearson, N.M., and Jegalian, K. 2001. The human Y chromosome, in the light of evolution. Nat. Rev. Genet. 2: 207-216.
30. Lippman, Z., Gendrel, A., Black, M., Vaughn, M., Dedhia, N., McCombie, W., Lavine, K., Mittal, V., May, B., Kasschau, K., et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
31. Lucchesi, J.C. 1978. Gene dosage compensation and the evolution of sex chromosomes. Science 202: 711-716.
32. MacKnight, R.H. 1939. The sex-determining mechanism of Drosophila miranda. Genetics 24: 180-201.
33. Marin, I., Franke, A., Bashaw, G.J., and Baker, B.S. 1996. The dosage compensation system of Drosophila is co-opted by newly evolved X chromosomes. Nature 383: 160-163.
34. Mathiopoulos, K., della Torre, A., Predazzi, V., Petrarca, V., and Coluzzi, M. 1998. Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction. Proc. Natl. Acad. Sci. 95: 12444-12449.
35. Muller, H.J. 1940. Bearings of the Drosophila work on systematics. In The new systematics (ed. J.S. Huxley), pp. 185-268. Oxford University Press, London.
36. Ohno, S. 1967. Sex chromosomes and sex linked genes. Springer Verlag, Berlin.
37. Orr, H.A. and Kim, Y. 1998. An adaptive hypothesis for the evolution of the Y chromosome. Genetics 150: 1693-1698.
38. Peichel, C., Ross, J., Matson, C., Dickson, M., Grimwood, J., Schmutz, J., Myers, R., Mori, S., Schluter, D., and Kingsley, D. 2004 The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome. Curr. Biol. 14: 1416-1424.
39. Puig, M., Cáceres, M., and Ruiz, A. 2004. Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA. Proc. Natl. Acad. Sci. 101: 9013-9018.
40. Rice, W.R. 1996. Evolution of the Y sex chromosome in animals. BioScience 46: 331-343.
41. Richards, S., Liu, Y., Bettencourt, B.R., Hradecky, P., Letovsky, S., Nielsen, R., Thornton, K., Hubisz, M.J., Chen, R., Meisel, R.P., et al. 2005. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res. 15: 1-18.
42. Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
43. Saxena, R., Brown, L., Hawkins, T., Alagappan, R., Skaletsky, H., Reeve, M., Reijo, R., Rozen, S., Dinulos, M., Disteche, C., et al. 1996. The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned. Nat. Genet. 14: 292-299.
44. Schotta, G., Ebert, A., Dorn, R., and Reuter, G. 2003. Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin. Cell Dev. Biol. 14: 67-75.
45. Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P.J., Cordum, H.S., Hillier, L., Brown, L.G., Repping, S., Pyntikova, T., Ali, J., Bieri, T., et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825-837.
46. Steinemann, M. and Steinemann, S. 1993. A duplication including the Y allele of Lcp2 and the TRIM retrotransposon at the Lcp locus on the degenerating neo-Y chromosome of Drosophila miranda: Molecular structure and mechanisms by which it may have arisen. Genetics 134: 497-505.
47. _. 1998. Enigma of Y chromosome degeneration: neo-Y and neo-X chromosomes of Drosophila miranda: A model for sex chromosome evolution. Genetica 102-103: 409-420.
48. Waters, P.D., Duffy, B., Frost, C.J., Delbridge, M.L., and Graves, J.A. 2001. The human Y chromosome derives largely from a single autosomal region added to the sex chromosomes 80-130 million years ago. Cytogenet. Cell Genet. 92: 74-79.
49. Wyckoff, G.J., Li, J., and Wu, C.I. 2002. Molecular evolution of functional genes on the mammalian Y chromosome. Mol. Biol. Evol. 19: 1633-1636.
50. http://flybase.bio.indiana.edu/blast/; FlyBase.
51. http://www.ebi.ac.uk/Wise2/; Wise2.
52. http://www.girinst.org/Censor_Server.html; Repbase.