Nonrandom gene loss from the drosophila miranda neo-Y chromosome

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 1329-1337

  Kaiser, Vera B ^a   Zhou, Qi ^a   Bachtrog, Doris ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Degeneration; Drosophila pseudoobscura; Evolution; Sex chromosomes; Sex biased gene expression; Tissue specificity

Indexed keywords

DROSOPHILA MIRANDA; DROSOPHILA PSEUDOOBSCURA;

ANIMAL; ARTICLE; DROSOPHILA; FEMALE; GENETICS; MALE; METHODOLOGY; MOLECULAR EVOLUTION; SEQUENCE ANALYSIS; Y CHROMOSOMAL INHERITANCE; Y CHROMOSOME;

ANIMALS; DROSOPHILA; EVOLUTION, MOLECULAR; FEMALE; GENES, Y-LINKED; MALE; SEQUENCE ANALYSIS, RNA; Y CHROMOSOME;

EID: 84858961873     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr103     Document Type: Article

References (33)

1. Abascal F, Zardoya R, Telford MJ. 2010. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38:W7-W13.
2. Bachtrog D. 2006. Expression profile of a degenerating neo-Y chromosome in Drosophila. Curr Biol. 16:1694-1699. (Pubitemid 44691786)
3. Bachtrog D, Charlesworth B. 2002. Reduced adaptation of a non-recombining neo-Y chromosome. Nature 416:323-326. (Pubitemid 34260246)
4. Bachtrog D, Hom E, Wong KM, Maside X, de Jong P. 2008. Genomic degradation of a young Y chromosome in Drosophila miranda. Genome Biol. 9:R30.
5. Bartolomé C, Charlesworth B. 2006. Evolution of amino-acid sequences and codon usage on the Drosophila miranda neo-sex chromosomes. Genetics 174:2033-2044. (Pubitemid 46011592)
6. Bone JR, Kuroda MI. 1996. Dosage compensation regulatory proteins and the evolution of sex chromosomes in Drosophila. Genetics 144:705-713. (Pubitemid 26325861)
7. Bull JJ. 1983. Evolution of sex determining mechanisms. Menlo Park (CA): Benjamin Cummings.
8. Carvalho AB, Koerich LB, Clark AG. 2009. Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet. 25:270-277.
9. Charlesworth B. 1996. The evolution of chromosomal sex determination and dosage compensation. Curr Biol. 6:149-162.
10. Charlesworth B, Betancourt AJ, Kaiser VB, Gordo I. 2009. Genetic recombination and molecular evolution. Cold Spring Harb Symp Quant Biol. 74:177-186.
11. Charlesworth B, Charlesworth D. 2000. The degeneration of Y chromosomes. Philos Trans R Soc Lond B Biol Sci. 355:1563-1572.
12. Chibalina MV, Filatov DA. 2011. Plant Y chromosome degeneration is retarded by haploid purifying selection. Curr Biol. 21:1475-1479.
13. Dobzhansky T. 1935. Drosophila miranda, a New Species. Genetics 20:377-391.
14. Felsenstein J. 1974. Evolutionary advantage of recombination. Genetics 78:737-756.
15. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science 296:750-752. (Pubitemid 34442006)
16. Gout JF, Kahn D, Duret L. 2010. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PloS Genet. 6:e1000944.
17. Innocenti P, Morrow EH. 2010. The sexually antagonistic genes of Drosophila melanogaster. PLoS Biol. 8:e1000335.
18. Jiang ZF, Machado CA. 2009. Evolution of sex-dependent gene expression in three recently diverged species of Drosophila. Genetics 183:1175-1185.
19. Kaiser VB, Charlesworth B. 2010. Muller's Ratchet and the degeneration of the Drosophila miranda neo-Y chromosome. Genetics 185:339-348.
20. Larschan E, et al. 2011. X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature 471:115-118.
21. Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol Biol Evol. 22:1345-1354. (Pubitemid 40577773)
22. Papp B, Pal C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197. (Pubitemid 36858686)
23. Qian W, Zhang J. 2008. Gene dosage and gene duplicability. Genetics 179:2319-2324.
24. Rice WR. 1984. Sex-chromosomes and the evolution of sexual dimorphism. Evolution 38:735-742.
25. Seoighe C, Wolfe KH. 1999. Yeast genome evolution in the postgenome era. Curr Opin Microbiol. 2:548-554. (Pubitemid 29477185)
26. Skaletsky H, et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423:825-837. (Pubitemid 36781267)
27. Steinemann M, Steinemann S. 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. (Pubitemid 28376701)
28. Straub T, Becker PB. 2011. Transcription modulation chromosome-wide: universal features and principles of dosage compensation in worms and flies. Curr Opin Genet Dev. 21:147-153.
29. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111.
30. Trapnell C, et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28:511-515.
31. Yanai I, et al. 2005. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bio-informatics 21:650-659. (Pubitemid 40424791)
32. Yi S, Charlesworth B. 2000. Contrasting patterns of molecular evolution of the genes on the new and old sex chromosomes of Drosophila miranda. Mol Biol Evol. 17:703-717. (Pubitemid 30252258)
33. Yu J, Pacifico S, Liu G, Finley RL Jr. 2008. DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9:461.