Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila

Genome Biology

Volumn 8, Issue 1, 2007, Pages

  Bai, Yongsheng ^a   Casola, Claudio ^a   Feschotte, Cédric ^a   Betrán, Esther ^a  

^a UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE DELETION; GENE IDENTIFICATION; GENE SEQUENCE; GENOMICS; INSECT GENETICS; MOLECULAR EVOLUTION; NONHUMAN; RETROPOSON; SPECIES DIFFERENCE; ANIMAL; CHIMERA; COMPARATIVE STUDY; DNA SEQUENCE; GENE; GENETICS; MALE; METABOLISM; PHYLOGENY; TESTIS;

DROSOPHILA MELANOGASTER; PRIMATES;

ANIMALS; CHIMERISM; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENES, INSECT; GENOMICS; MALE; PHYLOGENY; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; TESTIS;

EID: 34147128526     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-1-r11     Document Type: Article

References (52)

1. Brosius J Retroposons - seeds of evolution. Science 1991 251 753 10.1126/ science.1990437 1990437
2. Mighell AJ Smith NR Robinson PA Markham AF Vertebrate pseudogenes. FEBS Lett 2000 468 109-114 10.1016/S0014-5793(00)01199-6 10692568
3. Betrán E Long M Dntf-2r: A young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 2003 164 977-988 1462638 12871908
4. Emerson JJ Kaessmann H Betrán E Long M Extensive gene traffic on the mammalian X chromosome. Science 2004 303 537-540 10.1126/ science.1090042 14739461
5. Long M Langley CH Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 1993 260 91-95 10.1126/science.7682012 7682012
6. McCarrey JR Evolution of tissue-specific gene expression in mammals: How a new phosphoglycerate kinase was formed and refined. BioScience 1994 44 20-27 10.2307/1312402
7. Devor EJ Primate microRNAs miR-220 and miR-492 lie within processed pseudogenes. J Hered 2006 97 186-190 10.1093/jhered/esj022 16489141
8. Nozawa M Aotsuka T Tamura K A novel chimeric gene, siren, with retroposed promoter sequence in the Drosophila bipectinata complex. Genetics 2005 171 1719-1727 1456098 16143626 10.1534/genetics.105.041699
9. Zhang Z Harrison PM Liu Y Gerstein M Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 2003 13 2541-2558 403796 14656962 10.1101/ gr.1429003
10. Harrison PM Milburn D Zhang Z Bertone P Gerstein M Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res 2003 31 1033-1037 149191 12560500 10.1093/nar/gkg169
11. Petrov D Hartl DL Pseudogene evolution and natural selection for a compact genome. J Hered 2000 91 221-227 10.1093/jhered/91.3.221 10833048
12. Marques AC Dupanloup I Vinckenbosch N Reymond A Kaessmann H Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 2005 3 e357 1251493 16201836 10.1371/journal.pbio.0030357
13. Betrán E Thornton K Long M Retroposed new genes out of the X in Drosophila. Genome Res 2002 12 1854-1859 187566 12466289 10.1101/gr.6049
14. van Daal A White EM Elgin SC Gorovsky MA Conservation of intron position indicates separation of major and variant H2As is an early event in the evolution of eukaryotes. J Mol Evol 1990 30 449-455 10.1007/BF02101116 2111857
15. Zhang Z Inomata N Yamazaki T Kishino H Evolutionary history and mode of the amylase multigene family in Drosophila. J Mol Evol 2003 57 702-709 10.1007/s00239-003-2521-7 14745539
16. Soares MB Schon E Henderson A Karathanasis SK Cate R Zeitlin S Chirgwin J Efstratiadis A RNA-mediated gene duplication: The rat preproinsulin I gene is a functional retroposon. Mol Cell Biol 1985 5 2090-2103 366927 2427930
17. Luan DD Korman MH Jakubczak JL Eickbush TH Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition. Cell 1993 72 595-605 10.1016/ 0092-8674(93)90078-5 7679954
18. Esnault C Maestre J Heidmann T Human LINE retrotransposons generate processed pseudogenes. Nat Genet 2000 24 363-367 10.1038/74184 10742098
19. Brosius J Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet 1999 15 304-305 10.1016/S0168-9525(99)01783-7 10431191
20. Brosius J Gould SJ On "genomenclature": A comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proc Natl Acad Sci USA 1992 89 10706 10710 50410 1279691 10.1073/ pnas.89.22.10706
21. Tamura K Subramanian S Kumar S Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 2004 21 36-44 10.1093/molbev/msg236 12949132
22. Sokal RR Rohlf FJ Biometry New York: Freeman 3 1995
23. Zhang Z Gerstein M Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev 2004 14 328-335 10.1016/j.gde.2004.06.003 15261647
24. Wang PJ Page DC Functional substitution for TAF(II)250 by a retroposed homolog that is expressed in human spermatogenesis. Hum Mol Genet 2002 11 2341-2346 10.1093/hmg/11.19.2341 12217962
25. Lifschytz E Lindsley DL The role of X-chromosome inactivation during spermatogenesis (Drosophila-allocycly-chromosome evolution-male sterility-dosage compensation). Proc Natl Acad Sci USA 1972 69 182-186 427571 4621547 10.1073/pnas.69.1.182
26. Ranz JM Castillo-Davis CI Meiklejohn CD Hartl DL Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 2003 300 1742-1745 10.1126/science.1085881 12805547
27. Parisi M Nuttall R Naiman D Bouffard G Malley J Andrews J Eastman S Oliver B Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 2003 299 697-700 1363366 12511656 10.1126/science.1079190
28. Wu C-I Xu EY Sexual antagonism and X inactivation - the SAXI hypothesis. Trends Genet 2003 19 243-247 10.1016/S0168-9525(03)00058-1 12711214
29. FlyBase http://flybase.bio.indiana.edu
30. Yuan X Miller M Belote JM Duplicated proteasome subunit genes in Drosophila melanogaster encoding testes-specific isoforms. Genetics 1996 144 147-157 1207488 8878681
31. Ma J Katz E Belote JM Expression of proteasome subunit isoforms during spermatogenesis in Drosophila melanogaster. Insect Mol Biol 2002 11 627-639 10.1046/j.1365-2583.2002.00374.x 12421421
32. Vinckenbosch N Dupanloup I Kaessmann H Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 2006 103 3220-3225 1413932 16492757 10.1073/pnas.0511307103
33. Zhang Z Harrison P Gerstein M Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 2002 12 1466-1482 187539 12368239 10.1101/gr.331902
34. Meinhardt A Wilhelm B Seitz J Expression of mitochondrial marker proteins during spermatogenesis. Hum Reprod Update 1999 5 108-119 10.1093/humupd/5.2.108 10336016
35. Hwa JJ Zhu AJ Hiller MA Kon CY Fuller MT Santel A Germ-line specific variants of components of the mitochondrial outer membrane import machinery in Drosophila. FEBS Lett 2004 572 141-146 10.1016/ j.febslet.2004.07.025 15304338
36. Timakov B Zhang P The hsp60B gene of Drosophila melanogaster is essential for the spermatid individualization process. Cell Stress Chaperones 2001 6 71-77 434385 11525246 10.1379/ 1466-1268(2001)006<0071:THGODM>2.0.CO;2
37. Masly JP Jones CD Noor MA Locke J Orr HA Gene transposition as a cause of hybrid sterility in Drosophila. Science 2006 313 1448-1450 10.1126/ science.1128721 16960009
38. Pavlicek A Gentles AJ Paces J Paces V Jurka J Retroposition of processed pseudogenes: The impact of RNA stability and translational control. Trends Genet 2006 22 69-73 1379630 16356584 10.1016/j.tig.2005.11.005
39. Betrán E Bai Y Motiwale M Fast protein evolution and germline expression of a Drosophila parental gene and its young retroposed paralog. Mol Biol Evol 2006 23 2191-2202 10.1093/molbev/msl090 16916943
40. Bradley J Baltus A Skaletsky H Royce-Tolland M Dewar K Page DC An X-to-autosome retrogene is required for spermatogenesis in mice. Nat Genet 2004 36 872-876 10.1038/ng1390 15258580
41. Rohozinski J Bishop CE The mouse juvenile spermatogonial depletion (jsd) phenotype is due to a mutation in the X-derived retrogene, mUtp14b. Proc Natl Acad Sci USA 2004 101 11695-11700 511039 15289605 10.1073/ pnas.0401130101
42. Pearson WR Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 2000 132 185-219 10547837
43. Berkeley Drosophila Genome Project: Release 4 http://www.fruitfly.org/ annot/release4.html
44. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997 25 3389-3402 146917 9254694 10.1093/nar/ 25.17.3389
45. Li WH Sadler LA Low nucleotide diversity in man. Genetics 1991 129 513-523 1204640 1743489
46. Yang Z Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 1998 15 568-573 9580986
47. Assembly/Alignment/Annotation of 12 related Drosophila species: Comparative Analysis Freeze 1 http://rana.lbl.gov/drosophila;
48. Adams MD Celniker SE Holt RA Evans CA Gocayne JD Amanatides PG Scherer SE Li PW Hoskins RA Galle RF et al. The genome sequence of Drosophila melanogaster. Science 2000 287 2185-2195 10.1126/science.287.5461.2185 10731132
49. Richards S Liu Y Bettencourt BR Hradecky P Letovsky S Nielsen R Thornton K Hubisz MJ Chen R Meisel RP et al. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res 2005 15 1-18 540289 15632085 10.1101/gr.3059305
50. Powell JR Progress and Prospects in Evolutionary Biology: The Drosophila Model New York: Oxford University Press 1 1997
51. UCSC Browser http://genome.ucsc.edu
52. Kumar S Tamura K Nei M MEGA: Molecular evolutionary genetics software for microcomputers. Comput Appl Biosci 1994 10 189-191 8019868