Evolution at the subgene level: Domain rearrangements in the Drosophila phylogeny

Molecular Biology and Evolution

Volumn 29, Issue 2, 2012, Pages 689-705

  Wu, Yi Chieh ^a   Rasmussen, Matthew D ^a   Kellis, Manolis ^a,b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

domain and architecture evolution; gene fusion and fission; phylogenetics

Indexed keywords

ALGORITHM; ARTICLE; CLADISTICS; DROSOPHILA; GENE DUPLICATION; GENE EVOLUTION; GENE FUSION; GENE LOSS; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC PARAMETERS; NONHUMAN; PHYLOGENY;

ALGORITHMS; ANIMALS; BIOLOGICAL EVOLUTION; DROSOPHILA; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE FUSION; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RNA, MESSENGER;

EID: 84862907907     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr222     Document Type: Article

References (85)

1. Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, Novik A, Sorek R. 2006. Transcription-mediated gene fusion in the human genome. Genome Res. 16:30-36. (Pubitemid 43048931)
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
3. Apic G, Gough J, Teichmann SA. 2001. An insight into domain combinations. Bioinformatics 17:S83-S89. (Pubitemid 33793497)
4. Apic G, Huber W, Teichmann SA. 2003. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J Struct Funct Genomics 4:67-78. (Pubitemid 37356260)
5. Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. JACM 56:1-44.
6. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy S, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer ELL. 2002. The Pfam protein families database. Nucleic Acids Res. 30:276-280. (Pubitemid 34679563)
7. Behzadi B, Vingron M. 2006. Reconstructing domain compositions of ancestral multi-domain proteins. In: Bourque G, El-Mabrouk N, editors. Comparative genomics. Lecture Notes in Computer Science. Vol. 4205. Berlin-Heidelberg (Germany): Springer. p. 1-10. (Pubitemid 44618794)
8. Bhattacharyya RP, Reményi A, Yeh BJ, Lim WA. 2006. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem. 75:655-680. (Pubitemid 44118047)
9. Bornberg-Bauer E, Beaussart F, Kummerfeld SK, Teichmann SA, Weiner J. 2005. The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci. 62:435-445. (Pubitemid 40379234)
10. Butler G, Rasmussen MD, Lin MF, et al. (51 co-authors). 2009. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459:657-662.
11. Chen K, Durand D, Farach-Colton M. 2000. NOTUNG: a program for dating gene duplications and optimizing gene family trees. J Comput Biol. 7:429-447.
12. Courseaux A, Nahon JL. 2001. Birth of two chimeric genes in the hominidae lineage. Science 291:1293-1297.
13. David LA, Alm EJ. 2011. Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469:93-96.
14. Durrens P, Nikolski M, Sherman D. 2008. Fusion and fission of genes define a metric between fungal genomes. PLoS Comput Biol. 4:e1000200.
15. Edgar R. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. (Pubitemid 38832724)
16. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8:163-167. (Pubitemid 28177226)
17. Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300:1706-1707. (Pubitemid 36712558)
18. Enright A, Ouzounis C. 2001. Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol. 2: research0034.1-research0034.7.
19. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-90.
20. Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584. (Pubitemid 34679732)
21. Felsenstein J. 1981. Evolutionary trees from dna sequences: a maximum likelihood approach. J Mol Evol. 17:368-376. (Pubitemid 11016207)
22. Fong JH, Geer LY, Panchenko AR, Bryant SH. 2007. Modeling the evolution of protein domain architectures using maximum parsimony. J Mol Biol. 366:307-315. (Pubitemid 46123330)
23. Forslund K, Henricson A, Hollich V, Sonnhammer ELL. 2008. Domain tree-based analysis of protein architecture evolution. Mol Biol Evol. 25:254-264. (Pubitemid 351231600)
24. Goodman M, Czelusniak J, Moore G, Romero-Herrera A, Matsuda G. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool. 28:132-163.
25. Gough J. 2005. Convergent evolution of domain architectures (is rare). Bioinformatics 21:1464-1471. (Pubitemid 40552751)
26. Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. 2005. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15:1153-1160. (Pubitemid 41126871)
27. Hahn MW, Demuth JP, Han SG. 2007. Accelerated rate of gene gain and loss in primates. Genetics 177:1941-1949. (Pubitemid 350277083)
28. Hahn MW, Han MV, Han SG. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3:e197.
29. Han JDJ, Dupuy D, Bertin N, Cusick ME, Vidal M. 2005. Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol. 23:839-844. (Pubitemid 43093127)
30. Heger A, Holm L. 2003. Exhaustive enumeration of protein domain families. J Mol Biol. 328:749-767. (Pubitemid 36438586)
31. Huang X, Miller W. 1991. A time-efficient, linear-space local similarity algorithm. Adv Appl Math. 12:337-357.
32. Hunter S, Apweiler R, Attwood TK, et al. (38 co-authors). 2009. Inter-Pro: the integrative protein signature database. Nucleic Acids Res. 37:D211-D215.
33. Jones CD, Begun DJ. 2005. Parallel evolution of chimeric fusion genes. Proc Natl Acad Sci U S A. 102:11373-11378. (Pubitemid 41153827)
34. Jones CD, 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. (Pubitemid 40799984)
35. Kaessmann H, Zöllner S, Nekrutenko A, Li WH. 2002. Signatures of domain shuffling in the human genome. Genome Res. 12:1642-1650. (Pubitemid 35363668)
36. Kummerfeld SK, Teichmann SA. 2005. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet. 21:25-30. (Pubitemid 40178845)
37. Lee B. 2009. Comparison of exon-boundary old and young domains during metazoan evolution. Genomics Inform. 7:131-135.
38. Liu M, Grigoriev A. 2004. Protein domains correlate strongly with exons in multiple eukaryotic genomes-evidence of exon shuffling? Trends Genet. 20:399-403. (Pubitemid 39094566)
39. Long M, Betran E, Thornton K, Wang W. 2003. The origin of new genes: glimpses from the young and old. Nat Rev Genet. 4:865-875. (Pubitemid 37345613)
40. Long M, Langley CH. 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260:91-95. (Pubitemid 23122751)
41. Long M, Rosenberg C, Gilbert W. 1995. Intron phase correlations and the evolutionof the intron/exonstructure of genes. Proc Natl Acad Sci U S A. 92:12495-12499. (Pubitemid 26014096)
42. Long M, Wang W, Zhang J. 1999. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 238:135-141. (Pubitemid 29437409)
43. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
44. Marchler-Bauer A, Anderson JB, Cherukuri PF, et al. (24 co-authors). 2005. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33:D192-D196. (Pubitemid 40207858)
45. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-753.
46. Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. 2008. Arrangements in the modular evolution of proteins. Trends Biochem Sci. 33:444-451.
47. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247:536-540.
48. Niimura Y, Nei M. 2007. Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2:e708.
49. Ohno S. 1970. Evolution by gene duplication. New York: Springer-Verlag.
50. Page RDM. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst Biol. 43:58-77. (Pubitemid 24979624)
51. Pasek S, Risler JL, Brézellec P. 2006. Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins. Bioinformatics 22:1418-1423. (Pubitemid 43985310)
52. Patthy L. 1987. Intron-dependent evolution: preferred types of exons and introns. FEBS Lett. 214:1-7.
53. Peisajovich SG, Garbarino JE, Wei P, Lim WA. 2010. Rapid diversification of cell signaling phenotypes by modular domain recombination. Science 328:368-372.
54. Ponting CP, Russell RR. 2002. The natural history of protein domains. Annu Rev Biophys Biomol Struct. 31:45-71. (Pubitemid 34666825)
55. Przytycka T, Davis G, Song N, Durand D. 2006. Graph theoretical insights into evolution of multidomain proteins. J Comput Biol. 13:351-363.
56. Rabenstein MD, Zhou S, Lis JT, Tjian R. 1999. Tata box-binding protein (tbp)-related factor2 (trf2), a third member of the tbp family. Proc Natl Acad Sci U S A. 96:4791-4796. (Pubitemid 29214490)
57. Rasmussen MD, Kellis M. 2007. Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes. Genome Res. 17:1932-1942. (Pubitemid 351369026)
58. Rasmussen MD, Kellis M. 2011. A Bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol. 28:273-290.
59. Rogers RL, Bedford T, Hartl DL. 2009. Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster. Genetics 181:313-322.
60. Rogers RL, Bedford T, Lyons AM, Hartl DL. 2010. Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proc Natl Acad Sci U S A. 107:10943-10948.
61. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
62. Schultz J, Milpetz F, Bork P, Ponting CP. 1998. Smart, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl. Acad. Sci. U. S. A. 95:5857-5864. (Pubitemid 28248931)
63. Shih HJ, Jones CD. 2008. Patterns of amino acid evolution in Drosophila ananassae chimeric gene, siren, parallel those of other Adh-derived chimeras. Genetics 180:1261-1263.
64. Snel B, Bork P, Huynen M. 2000. Genome evolution: gene fusion versus gene fission. Trends Genet. 16:9-11. (Pubitemid 30062226)
65. Song N, Joseph JM, Davis GB, Durand D. 2008. Sequence similarity network reveals common ancestry of multidomain proteins. PLoS Comput Biol. 4:e1000063.
66. Suhre K, Claverie JM. 2004. FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res. 32:D273-D276. (Pubitemid 38081655)
67. Sumita K, Makino Y, Katoh K, Kishimoto T, Muramatsu M, Mikoshiba K, Tamura T. 1993. Structure of a mammalian TBP (TATA-binding protein) gene: isolation of the mouse TBP genome. Nucleic Acids Res. 21:2769. (Pubitemid 23209181)
68. Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol. 21:36-44. (Pubitemid 38233516)
69. Thomson TM, Lozano JJ, Loukili N, et al. (14 co-authors). 2000. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. Genome Res. 10:1743-1756.
70. Uchiyama I. 2006. Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. Nucleic Acids Res. 34:647-658. (Pubitemid 43240251)
71. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. 2009. EnsemblCompara GeneTrees: complete, duplicationaware phylogenetic trees in vertebrates. Genome Res. 19:327-335.
72. Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA. 2004. Supradomains: evolutionary units larger than single protein domains. J Mol Biol. 336:809-823. (Pubitemid 38183030)
73. Wang W, Brunet FG, Nevo E, Long M. 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc Natl Acad Sci U S A. 99:4448-4453. (Pubitemid 34286005)
74. Wang W, Yu H, Long M. 2004. Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat Genet. 36:523-527. (Pubitemid 38620040)
75. Wang W, Zhang J, Alvarez C, Llopart A, 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.
76. Wang W, Zheng H, Fan C, et al. (14 co-authors). 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18:1791-1802. (Pubitemid 44260178)
77. Wapinski I, Pfeffer A, Friedman N, Regev A. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449:54-61. (Pubitemid 47373776)
78. Weiner J, Beaussart F, Bornberg-Bauer E. 2006. Domain deletions and substitutions in the modular protein evolution. FEBS J. 273:2037-2047.
79. Weiner J, Bornberg-Bauer E. 2006. Evolution of circular permutations in multidomain proteins. Mol Biol Evol. 23:734-743.
80. Wiedenhoeft J, Krause R, Eulenstein O. 2011. The plexus model for the inference of ancestral multi-domain proteins. IEEE/ACM Trans Comput Biol Bioinform. 8:890-901.
81. Xiao H, Friesen JD, Lis JT. 1995. Recruiting TATA-binding protein to a promoter: transcriptional activation without an upstream activator. Mol Cell Biol. 15:5757-5761.
82. Yanai I, Wolf Y, Koonin E. 2002. Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol. 3:research0024.1-research0024. 13.
83. Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, Li X, Ding Y, Yang S, Wang W. 2008. On the origin of new genes in Drosophila. Genome Res. 18:1446-1455.
84. Zmasek CM, Eddy SR. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17:821-828. (Pubitemid 32970480)
85. Zmasek CM, Eddy SR. 2002. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3:14.