A new retroposed gene in Drosophila heterochromatin detected by microarray-based comparative genomic hybridization

Journal of Molecular Evolution

Volumn 64, Issue 2, 2007, Pages 272-283

  Fan, Chuanzhu ^a   Long, Manyuan ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Drosophila; Heterochromatin; Ifc 2h; Microarray based comparative genomic hybridization; Retroposition; Selection sweep

Indexed keywords

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA MICROARRAY; DROSOPHILA; DROSOPHILA MAURITIANA; DROSOPHILA SECHELLIA; DROSOPHILA SIMULANS; FEMALE; GENE EXPRESSION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; HETEROCHROMATIN; MALE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; REGULATORY SEQUENCE;

ANIMALS; BASE SEQUENCE; BLOTTING, SOUTHERN; DNA; DROSOPHILA; GENE AMPLIFICATION; HETEROCHROMATIN; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; RETROELEMENTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

DROSOPHILA MAURITIANA; DROSOPHILA SECHELLIA; DROSOPHILA SIMULANS;

EID: 33846422742     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-006-0169-9     Document Type: Article

References (58)

1. Barrett M, Scheffer A, Ben-Dor A, et al. (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci USA 101:17765-17770
2. Begun D (1997) Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics 145:375-382
3. Bernard P, Maure JF, Partridge JF, Genier S, Javerzat JP, Allshire RC (2001) Requirement of heterochromatin for cohesion at centromeres. Science 294:2539-2542
4. Betran E, Long M (2003) Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164:977-988
5. Betran E, Thornton K, Long M (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12:1854-1859
6. Braverman J, Lazzaro BP, Aguade M, Langley CH (2005) DNA sequence polymorphism and divergence at the erect wing and suppressor of sable loci of Drosophila melanogaster and D. simulans. Genetics 170:1153-1165
7. Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289-1303
8. Choo K (2001) Domain organization at the centromere and neocentromere. Dev Cell 1:165-177
9. Dillon N (2004) Heterochromatin structure and function. Biol Cell 96:631-637
10. Fu Y, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709
11. Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20:307-315
12. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725-736
13. Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL (2004) 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14:179-187
14. Hoskins R, Smith CD, Carlson JW, et al. (2002) Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol 3:RESEARCH0085
15. Hudson R (1990) Gene genealogies and the coalescent process. Oxf Surv Evol Biol 7:1-42
16. Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164
17. Inoue K, Dewar K, Katsanis N, Reiter LT, Lander ES, Devon KL, Wyman DW, Lupski JR, Birren B (2001) The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes. Genome Res 11:1018-1033
18. Jones C, Begun DJ (2005) Parallel evolution of chimeric fusion genes. Proc Natl Acad Sci USA 102:11373-11378
19. Jones C, Custer AW, Begun DJ (2005) Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche. Genetics 170:207-219
20. Kreitman M, Hudson RR (1991) Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics 127:565-582
21. Lachaise D, Cariou ML, David JR, Lemeunier F, Tsacas L (1988) Historical biogeography of the Drosophila melanogaster species subgroup. Evol Biol 22:159-225
22. Lachaise D, Harry M, Solignac M, Lemeunier F, Benassi V, Cariou ML (2000) Evolutionary novelties in island: Drosophila santomea, a new melanogaster sister species from Sao Tome. Proc R Soc Lond Ser B 267:1487-1495
23. Liu Y, Whittier RF (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25:674-681
24. Long M, Langley CH (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260:91-95
25. Loppin B, Lepetit D, Dorus S, Couble P, Karr TL (2005) Origin and neofunctionalization of a Drosophila paternal effect gene essential for zygote viability. Curr Biol 15:87-93
26. Makalowski W (2003) Genomics. Not junk after all. Science 300:1246-1247
27. Marchant G, Holm DG (1988) Genetic analysis of the heterochromatin of chromosome 3 in Drosophila melanogaster. II. Vital loci identified through EMS mutagenesis. Genetics 120:519-532
28. McVean GAT, Charlesworth B (2000) The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155:929-944
29. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
30. Nordborg M, Charlesworth B, Charlesworth D (1996) The effect of recombination on background selection. Genet Res 67:159-174
31. Nurminsky D, Nurminskaya MV, De Aguiar D, Hartl DL (1998) Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396:572-575
32. Ohler U, Liao G, Niemann H, Rubin GM (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol 3:research0087.1- 0087.12
33. Ohno S (1970) Evolution by gene duplication. Springer, Berlin
34. Petrov D (2001) Evolution of genome size: new approaches to an old problem. Trends Genet 17:23-28
35. Petrov D, Lozovskaya ER, Hartl DL (1996) High intrinsic rate of DNA loss in Drosophila. Nature 384:346-349
36. Pinkel D, Albertson DG (2005) Array comparative genomic hybridization and its applications in cancer. Nat Genet 37 (Suppl):S11-S17
37. Pinkel D, Segraves R, Sudar D, et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207-211
38. Powell J (1997) Progress and prospects in evolutionary biology: the Drosophila model. Oxford University Press, New York
39. Reese M (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26:51-56
40. Rozas J, Gullaud M, Blandin G, Aguadé M (2001) DNA variation at the rp49 gene region of Drosophila simulans: evolutionary inferences from an unusual haplotype structure. Genetics 158:1147-1155
41. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497
42. Rubin G, Yandell MD, Wortman JR, et al. (2000) Comparative genomics of the eukaryotes. Science 287:2204-2215
43. Schulze S, McAllister B, Sinclair D, Fitzpatrick K, Marchetti M, Pimpinelli S, Honda B (2006) Heterochromatic genes in Drosophila: A Comparative analysis of two genes. Genetics 173:1433-1445
44. Solidar A, Paschall JE, Malcom CM, Wyckoff GJ (2004) The SPEED toolkit: a resource for evolutionary analysis in human genetic studies. Am Soc Hum Gen Annu Meet, Toronto, Ontario, Canada, October
45. Swofford D (2002) PAUP: phylogenetic analysis using parsimony, version 4.0b10. Sinauer Associates, Sunderland, MA
46. Tajima F (1989) Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595
47. Thompson J, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
48. Wakimoto B, Hearn MG (1990) The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster. Genetics 125:141-154
49. Wang W, Brunet FG, Nero E, Long M (2002) Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc Natl Acad Sci USA 99:4448-4453
50. Wang W, Thornton K, Emerson JJ, Long M (2004a) Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics 166:1783-1794
51. Wang W, Yu H, Long M (2004b) Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat Genet 36:523-527
52. Watterson G (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256-276
53. Wu Z, Irizarry RA, Gentleman R, Murillo FM, Spencer F (2004) A model-based background adjustment for oligonucleotide expression arrays. Johns Hopkins Univ Dept Biostat Working Papers 1:1-26
54. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
55. Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568-573
56. Yasuhara J, DeCrease CH, Wakimoto BT (2005) Evolution of heterochromatic genes of Drosophila. Proc Natl Acad Sci USA 102:10958-10963
57. Yi S, Charlesworth B (2000) A selective sweep associated with a recent gene transposition in Drosophila miranda. Genetics 156:1753-1763
58. Zhang J, Dean AM, Brunet F, Long M (2004) Evolving protein functional diversity in new genes of Drosophila. Proc Natl Acad Sci USA 101:16246-16250