Large-Scale Gene and Ancient Genome Duplications

The Evolution of the Genome

Volumn , Issue , 2005, Pages 329-368

  Van De Peer, Yves ^a   Meyer, Axel ^b  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882516955     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012301463-4/50008-5     Document Type: Chapter

References (132)

1. Abi-Rached L, Gilles A, Shiina T, et al. Evidence of en bloc duplication in vertebrate genomes. Nat Genet 2002, 31:100-105.
2. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
3. Amores A, Force A, Yan YL, et al. Zebrafish hox clusters and vertebrate genome evolution. Science 1998, 282:1711-1714.
4. Anderson E Introgressive Hybridization 1949, Wiley, New York.
5. Aparicio S, Chapman J, Stupka E, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002, 297:1301-1310.
6. Aparicio S, Hawker K, Cottage A, et al. Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat Genet 1997, 16:79-83.
7. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815. Arabidopsis Genome Initiative.
8. Arnold ML Natural Hybridization and Evolution 1997, Oxford University Press, Oxford.
9. Bailey JA, Gu Z, Clark RA, et al. Recent segmental duplications in the human genome. Science 2002, 297:1003-1007.
10. Benton MJ Phylogeny of the major tetrapod groups: morphological data and divergence dates. J Mol Evol 1990, 30:409-424.
11. Blanc G, Barakat A, Guyot R, et al. Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 2000, 12:1093-1101.
12. Blanc G, Hokamp K, Wolfe KH A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 2003, 13:137-144.
13. Bowers JE, Chapman BA, Rong J, Paterson AH Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003, 422:433-438.
14. Brown TA Genomes 1999, BIOS Scientific Publishers, Oxford.
15. Calabrese PP, Chakravarty S, Vision TJ Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 2003, 19:S174-S180.
16. Carroll RL Vertebrate Paleontology and Evolution 1988, W. H. Freeman and Co., New York.
17. Cheng CHC, Chen L Evolution of an antifreeze glycoprotein. Nature 1999, 401:443-444.
18. Conery JS, Lynch M Nucleotide substitutions and the evolution of duplicate genes. Pac Symp Biocomput 2001, 167-178.
19. De Bodt S, Raes J, Florquin K, et al. Structural annotation and evolutionary analysis of type I MADS box transcription factors in plants. J Mol Evol 2003, 56:573-586.
20. Dietrich FS, Voegeli S, Brachat S, et al. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 2004, 304:304-307.
21. Duda TF, Palumbi SR Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc Natl Acad Sci USA 1999, 96:6820-6823.
22. Dujon B, Sherman D, Fisher G Genome evolution in yeasts. Nature 2004, 430:35-44.
23. Dulai KS, von Dornum M, Mollon JD, Hunt DM The evolution of trichromatic colour vision by opsin gene duplication in new world and old world primates. Genome Res 1999, 9:629-638.
24. Durand D Vertebrate evolution: doubling and shuffling with a full deck. Trends Genet 2003, 19:2-5.
25. Easteal S, Collet C Consistent variation in amino-acid substitution rate, despite uniformity of mutation rate: protein evolution in mammals is not neutral. Mol Biol Evol 1994, 11:643-647.
26. Ehrendorfer F Polyploidy and distribution. Polyploidy-Biological Relevance 1980, 45-60. Plenum Press, New York. W.H. Lewis (Ed.).
27. Endo T, Ikeo K, Gojobori T Large-scale search for genes on which positive selection may operate. Mol Biol Evol 1996, 13:685-690.
28. Escriva H, Manzon L, Youson J, Laudet V Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol Biol Evol 2002, 9:1440-1450.
29. Force A, Lynch M, Pickett FB, et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999, 151:1531-1545.
30. Fraser CM, Casjens S, Huang WM, et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 1997, 390:580-586.
31. Fried C, Prohaska SJ, Stadler PF Independent Hox-cluster duplications in lampreys. J Exp Zool (Mol Dev Evol) 2003, 299:18-25.
32. Friedman R, Hughes AL The temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol Biol Evol 2003, 20:154-161.
33. Furlong RF, Holland PWH Were vertebrates octoploids?. Philos Trans R Soc Lond B 2002, 357:531-544.
34. Gates MA, Kim L, Cardozo T, et al. A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res 1999, 9:334-347.
35. Gaut BS Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res 2001, 11:55-66.
36. Gehring WJ Master Control Genes in Development and Evolution: The Homeobox Story 1998, Yale University Press, New Haven, CT.
37. Gevers D, Vandepoele K, Simillion C, Van de Peer Y Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol 2004, 12:148-154.
38. Gibson TJ, Spring J Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins. Trends Genet 1998, 14:46-49.
39. Goff SA, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296:92-100.
40. Grant D, Cregan P, Shoemaker RC Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc Natl Acad Sci USA 2000, 97:4168-4173.
41. Gu X, Wang Y, Gu J Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat Genet 2002, 31:205-209.
42. Gu Z, Steinmetz LM, Gu X, et al. Role of duplicate genes in genetic robustness against null mutations. Nature 2003, 421:63-66.
43. Guo M, Davis D, Birchler JA, et al. Dosage effect on gene expression in a maize ploidy series. Genetics 1996, 142:1349-1355.
44. Guyot R, Keller B Ancestral genome duplication in rice. Genome 2004, 47:610-614.
45. Haldane JBS The part played by recurrent mutation in evolution. Am Nat 1933, 67:5-19.
46. Holland PW Vertebrate evolution: something fishy about Hox genes. Curr Biol 1997, 7:R570-R572.
47. Holland PW, Garcia-Fernandez J Hox genes and chordate evolution. Dev Biol 1996, 173:382-395.
48. Holland PW, Garcia-Fernandez J, Williams NA, Sidow A Gene duplications and the origins of vertebrate development. Development 1994, 120:125-133. (Suppl.).
49. Hughes AL Adaptive Evolution of Genes and Genomes 1999, Oxford University Press, Oxford.
50. Hughes AL Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J Mol Evol 1999, 48:565-576.
51. Hughes AL, da Silva J, Friedman R Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res 2001, 11:771-780.
52. Hughes AL, Green JA, Garbayo JM, Roberts RM Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proc Natl Acad Sci USA 2000, 97:3319-3323.
53. Irvine S, Carr JL, Bailey WJ, et al. Genomics analysis of Hox clusters in the sea lamprey Petromyzon marinus. J Exp Zool 2002, 249:47-62.
54. Jia L, Clegg MT, Jiang T Excess of non-synonymous substitutions suggest that positive selection episodes occurred during the evolution of DNA-binding domains in the Arabidopsis R2R3-MYB gene family. Plant Mol Biol 2003, 52:627-642.
55. Kellis M, Birren BW, Lander ES Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004, 428:617-624.
56. Kimura M The Neutral Theory of Molecular Evolution 1983, Cambridge University Press, Cambridge, UK.
57. Koszul R, Caburet S, Dujon B, Fischer G Eukaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J 2004, 23:234-243.
58. Ku HM, Vision T, Liu J, Tanksley SD Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 2000, 97:9121-9126.
59. Larhammar D, Lundin LG, Hallbook F The human Hox-bearing chromosome regions did arise by block or chromosome (or even genome) duplications. Genome Res 2002, 12:1910-1920.
60. Levy A, Feldman M The impact of polyploidy on grass genome evolution. Plant Physiol 2002, 130:1587-1593.
61. Li WH Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 1993, 36:96-99.
62. Li WH, Gu Z, Cavalcanti ARO, Nekrutenko A Detection of gene duplications and block duplication in eukaryotic genomes. J Struct Funct Genomics 2003, 3:27-34.
63. Lin X, Kaul S, Rounsley S, et al. Sequence and analysis of chromosome 2 of the plant Arbidopsis thaliana. Nature 1999, 402:761-768.
64. Lundin LG, Larhammar D, Hallbook F Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates. J Struct Funct Genomics 2003, 3:53-63.
65. Lynch M, Conery JS The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155.
66. Lynch M, Force A The probability of duplicate gene preservation by subfunctionalization. Genetics 2000, 154:459-473.
67. Málaga-Trillo E, Meyer A Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Am Zool 2001, 41:676-686.
68. Martin A Is tetralogy true? Lack of support for the "one-to-four rule". Mol Biol Evol 2001, 18:89-93.
69. Mayer K, Schüller C, Wambutt R, et al. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 1999, 402:769-777.
70. McLysaght A, Hokamp K, Wolfe KH Extensive genomic duplication during early chordate evolution. Nat Genet 2002, 31:200-204.
71. Messier W, Stewart CB Episodic adaptive evolution of primate lysosymes. Nature 1997, 385:151-154.
72. Meyer A Phylogenetic relationships and evolutionary processes in East African cichlids. Trends Ecol Evol 1993, 8:279-284.
73. Meyer A, Kocher TD, Basasibwaki P, Wilson A Monophyletic origin of Lake Victoria Africa cichlid fishes suggested by mitochondrial DNA sequences. Nature 1990, 347:550-663.
74. Meyer A, Schartl M Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol 1999, 11:699-704.
75. Naruse K, Fukamachi S, Mitani H, et al. A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics 2000, 154:1773-1784.
76. Nei M, Gojobori T Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3:418-426.
77. Nei M, Kumar S Molecular Evolution and Phylogenetics 2000, Oxford University Press, Oxford.
78. Nowak MA, Boerlijst MC, Cooke J, Maynard Smith J Evolution of genetic redundancy. Nature 1997, 388:167-171.
79. Ohno S Evolution by Gene Duplication 1970, Springer Verlag, New York.
80. Ohno S Ancient linkage groups and frozen accidents. Nature 1973, 244:259-262.
81. Osborn TC, Pires JC, Birchler JA, et al. Understanding mechanisms of novel gene expression in polyploids. Trends Genet 2003, 19:141-147.
82. Panopoulou G, Hennig S, Groth D, et al. New evidence for genome-wide duplications at the origin of vertebrates using an Amphioxus gene set and completed animal genomes. Genome Res 2003, 13:1056-1066.
83. Paterson AH, Bowers JE, Chapman BA Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 2004, 101:9903-9908.
84. Paterson AH, Lan TH, Reischmann KP, et al. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nat Genet 1996, 14:380-382.
85. Postlethwait JH, Woods IG, Ngo-Hazelett P, et al. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 2000, 10:1890-1902.
86. Prince VE, Pickett FB Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 2002, 3:827-837.
87. Raes J, Van de Peer Y Gene duplications, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico. Appl Bioinformatics 2003, 2:92-101.
88. Raes J, Vandepoele K, Simillion C, et al. Investigating ancient duplication events in the Arabidopsis genome. J Struct Func Genomics 2003, 3:117-129.
89. Ramsey J, Schemske DW Neopolyploidy in flowering plants. Annu Rev Ecol Syst 2002, 33:589-639.
90. Riehle MM, Bennette AF, Long AD Genetic architecture of thermal adaptation in Escherichia coli. Proc Natl Acad Sci USA 2001, 98:525-530.
91. Rieseberg LH, Raymond O, Rosenthal DM, et al. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 2003, 301:1211-1216.
92. Robinson-Rechavi M, Marchand O, Escriva H, et al. Euteleost fish genomes are characterized by expansion of gene families. Genome Res 2001, 11:781-788.
93. Robinson-Rechavi M, Marchand O, Escriva H, Laudet V An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes. Curr Biol 2001, 11:R458-R459.
94. Rost B Twilight zone of protein sequence alignments. Protein Eng 1999, 12:85-94.
95. Seoighe C, Wolfe KH Yeast genome evolution in the post-genome era. Curr Opin Microbiol 1999, 2:548-554.
96. Shu DG, Luo HL, Conway Morris S, et al. Lower Cambrian vertebrates from south China. Nature 1999, 402:42-46.
97. Simillion C, Vandepoele K, Saeys Y, Van de Peer Y Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res 2004, 14:1095-1106.
98. Simillion C, Vandepoele K, Van Montagu M, et al. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 2002, 99:13627-13632.
99. Skrabanek L, Wolfe KH Eukaryote genome duplication: where's the evidence?. Curr Opin Genet Dev 1998, 8:694-700.
100. Spring J Vertebrate evolution by interspecific hybridisations: are we polyploid?. FEBS Lett 1997, 400:2-8.
101. Spring J Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates. J Struct Funct Genomics 2003, 3:19-25.
102. Stephens SG Possible significance of duplication in evolution. Adv Genet 1951, 4:247-265.
103. Stiassny MLJ, Meyer A Cichlids of the African Rift Lakes. Sci Am 1999, 64-69. February.
104. Sturmbauer C, Meyer A Genetic divergence, speciation and morphological stasis in a lineage of African cichlid fishes. Nature 1992, 358:578-581.
105. Takezaki N, Rzhestky A, Nei M Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol 1995, 12:823-833.
106. Taylor J, Braasch I, Frickey T, et al. Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res 2003, 13:382-390.
107. Taylor JS, Van de Peer Y, Braasch I, Meyer A Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B 2001, 356:1661-1679.
108. Terai Y, Mayer WE, Klein J, et al. The effect of selection on a long wavelength-sensitive (LWS) opsin gene of Lake Victoria cichlid fishes. Proc Natl Acad Sci USA 2002, 99:15501-15506.
109. Terryn N, Heijnen L, De Keyser A, et al. Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett 1999, 445:237-245.
110. Van de Peer Y, Taylor JS, Braasch I, Meyer A The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J Mol Evol 2001, 53:436-446.
111. Van de Peer Y, Taylor JS, Meyer A Are all fishes ancient polyploids?. J Struct Funct Genomics 2003, 3:65-73.
112. Vandepoele K, De Vos W, Taylor JS, et al. Major events in the genome evolution of vertebrates: paranome age and size differs considerably between fishes and land vertebrates. Proc Natl Acad Sci USA 2004, 101:1638-1643.
113. Vandepoele K, Saeys Y, Simillion C, et al. A new tool for the automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res 2002, 12:1792-1801.
114. Vandepoele K, Simillion C, Van de Peer Y Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet 2002, 18:606-608.
115. Vandepoele K, Simillion C, Van de Peer Y Evidence that rice, and other cereals, are ancient aneuploids. Plant Cell 2003, 15:2192-2202.
116. Vandepoele K, Simillion C, Van de Peer Y The quest for genomic homology. Curr Genomics 2004, 5:299-308.
117. Vision TJ, Brown DG, Tanksley SD The origins of genomic duplications in Arabidopsis. Science 2000, 290:2114-2117.
118. Werth CR, Windham MD A model for divergent, allopatric speciation of polyploidy pteridophytes resulting from silencing of duplicate-gene expression. Am Nat 1991, 137:515-526.
119. Wilson AB, Noack-Kunnmann K, Meyer A Incipient speciation in sympatric Nicaraguan crater lake cichlid fishes: sexual selection versus ecological diversification. Proc R Soc Lond B 2000, 267:2133-2141.
120. Wittbrodt J, Meyer A, Schartl M More genes in fish?. BioEssays 1998, 20:511-512.
121. Wolfe KH Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2001, 2:333-341.
122. Wolfe KH, Shields DC Molecular evidence for an ancient duplication of the entire yeast genome. Nature 1997, 387:708-713.
123. Woods IG, Kelly PD, Chu F, et al. A comparative map of the zebrafish genome. Genome Res 2000, 10:1903-1914.
124. Yang Z PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556. (available at http://abacus.gene.ucl.ac.uk/software/paml.html).
125. Yang Z, Nielsen R Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000, 17:32-43.
126. Yokoyama S, Blow NS, Radlwimmer FB Molecular evolution of color vision of zebra finch. Gene 2000, 259:17-24.
127. Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92.
128. Zhang J, Nei M Positive selection in the evolution of mammalian interleukin-2 genes. Mol Biol Evol 2000, 17:1413-1416.
129. Zhang J, Rosenberg HF, Nei M Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci USA 1998, 95:3708-3713.
130. Zhang J, Zhang YP, Rosenberg HF Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet 2002, 30:411-415.
131. Zhu M, Yu X A primitive fish close to the common ancestor of tetrapods and lungfish. Nature 2002, 418:767-770.
132. Zhu M, Yu X, Janvier P A primitive fossil fish sheds light on the origin of bony fishes. Nature 1999, 397.