Subfunction partitioning, the teleost radiation and the annotation of the human genome

Trends in Genetics

Volumn 20, Issue 10, 2004, Pages 481-490

  Postlethwait, John ^a   Amores, Angel ^a   Cresko, William ^a   Singer, Amy ^a   Yan, Yi Lin ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; EVOLUTION; FISH; GENE DUPLICATION; GENE FUNCTION; GENOME ANALYSIS; NONHUMAN; ORTHOLOGY; PHENOTYPE; PLEIOTROPY; PRIORITY JOURNAL; RADIATION; REVIEW; TELEOST; TETRAPLOIDY; VERTEBRATE;

ANIMALS; BIODIVERSITY; DRUG DESIGN; EVOLUTION, MOLECULAR; FISHES; GENE DUPLICATION; GENOME, HUMAN; GENOMICS; HUMANS; PHYLOGENY; SPECIES SPECIFICITY; VARIATION (GENETICS);

TELEOST FISH; TELEOSTEI; VERTEBRATA;

EID: 4444340536     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2004.08.001     Document Type: Review

References (95)

1. J.S. Nelson Fishes of the World 1994 Wiley-Interscience
2. S. Ohno Evolution by Gene Duplication 1970 Springer Verlag
3. C. Ohno Ancient linkage groups and frozen accidents Nature 244 1973 259 262
4. M. Ekker Coordinate embryonic expression of three zebrafish engrailed genes Development 116 1992 1001 1010
5. V.E. Prince Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk Development 125 1998 407 420
6. Y. Van de Peer Wanda: a database of duplicated fish genes Nucleic Acids Res 30 2002 109 112
7. Postlethwait, J. Fish Development and Genetics: The Zebrafish and Medaka Models (Korzh, Z.G.a.V., ed.), World Scientific (in press)
8. A. Amores Zebrafish hox clusters and vertebrate genome evolution Science 282 1998 1711 1714
9. J. Postlethwait Vertebrate genome evolution and the zebrafish gene map Nat. Genet. 18 1998 345 349
10. M.A. Gates A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences Genome Res. 9 1999 334 347
11. W.B. Barbazuk The syntenic relationship of the zebrafish and human genomes Genome Res. 10 2000 1351 1358
12. J.H. Postlethwait Zebrafish comparative genomics and the origins of vertebrate chromosomes Genome Res. 10 2000 1890 1902
13. I.G. Woods A comparative map of the zebrafish genome Genome Res. 10 2000 1903 1914
14. J.S. Taylor Comparative genomics provides evidence for an ancient genome duplication event in fish Philos. Trans. R. Soc. Lond. B Biol. Sci 356 2001 1661 1679
15. Postlethwait, J. et al. (2002) Duplication of a portion of human chromosome 20q containing Topoisomerase (Top1) and Snail genes provides evidence on genome expansion and the radiation of teleost fish. In Aquatic Genomics: Steps Toward a Great Future (Shimizu, N. et al., eds), pp. 20-31, Springer-Verlag.
16. Y. Van de Peer Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes Gene 295 2002 205 211
17. J. Taylor Genome duplication, a trait shared by 22,000 species of ray-finned fish Genome Res. 13 2003 382 390
18. D.P. Locke Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization Genome Res. 13 2003 347 357
19. S. Ohno Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999 Semin. Cell Dev. Biol. 10 1999 517 522
20. D. Larhammar, and C. Risinger Molecular genetic aspects of tetraploidy in the common carp Cyprinus carpio Mol. Phylogenet. Evol. 3 1994 59 68
21. R. Phillips, and P. Rab Chromosome evolution in the Salmonidae (Pisces): an update Biol. Rev. Camb. Philos. Soc. 76 2001 1 25
22. L. David Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci Mol. Biol. Evol. 20 2003 1425 1434
23. J. Wittbrodt More genes in fish? BioEssays 20 1998 511 515
24. A. Meyer, and M. Schartl 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. 11 1999 699 704
25. B.S. Gaut, and J.F. Doebley DNA sequence evidence for the segmental allotetraploid origin of maize Proc. Natl. Acad. Sci. U. S. A. 94 1997 6809 6814
26. S. Aparicio Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes Nat. Genet. 16 1997 79 83
27. G. Vogel Doubled genes may explain fish diversity Science 281 1998 1119 1121
28. S. Aparicio Vertebrate evolution: recent perspectives from fish Trends Genet. 16 2000 54 56
29. S. Aparicio Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes Science 297 2002 1301 1310
30. A. Amores Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish Genome Res. 14 2004 1 10
31. S. Smith Identification and analysis of two snail genes in the pufferfish (Fugu rubripes) and mapping of human SNA to 20q Gene 247 2000 119 128
32. S.F. Smith Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q Genome Res. 12 2002 776 784
33. J. Altschmied Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish Genetics 161 2002 259 267
34. T. Toramoto Multiple gene organization of pufferfish Fugu rubripes tropomyosin isoforms and tissue distribution of their transcripts Gene 331 2004 41 51
35. P. Koopman Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes Gene 328 2004 177 186
36. R. Dildrop, and U. Ruther Organization of Iroquois genes in fish Dev. Genes Evol. 214 2004 26 276
37. D.M. Irwin A second insulin gene in fish genomes Gen. Comp. Endocrinol. 135 2004 150 158
38. K. Dethleffsen Insert-containing neurotrophins in teleost fish and their relationship to nerve growth factor Mol. Cell. Neurosci. 24 2003 380 394
39. M. Klinger Identification of Nogo-66 receptor (NgR) and homologous genes in fish Mol. Biol. Evol. 21 2004 76 85
40. J.C. Cardoso Isolation and characterisation of the corticotropin releasing factor receptor 1 (CRFR1) gene in a teleost fish, Fugu rubripes DNA Seq. 14 2003 215 218
41. W.P Yu Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu Trends Genet. 19 2003 180 183
42. K. Vandepoele Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates Proc. Natl. Acad. Sci. U. S. A. 101 2004 1638 1643
43. A. Christoffels Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes Mol. Biol. Evol. 21 2004 1146 1151
44. Y. Van de Peer Are all fishes ancient polyploids? J. Struct. Funct. Genomics 3 2003 65 73
45. K. Naruse A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping Genome Res. 14 2004 820 828
46. J.G. Inoue Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the 'ancient fish' Mol. Phylogenet. Evol. 26 2003 110 120
47. C.H. Chiu Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution Genome Res. 14 2004 11 17
48. G.J. Graham Tandem genes and clustered genes J. Theor. Biol. 175 1995 71 87
49. A. Force Preservation of duplicate genes by complementary, degenerative mutations Genetics 151 1999 1531 1545
50. A. Stoltzfus On the possibility of constructive neutral evolution J. Mol. Evol. 49 1999 169 181
51. J.H. Nadeau, and D. Sankoff Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution Genetics 147 1997 1259 1266
52. M.B. Hawkins Identification of a third distinct estrogen receptor and reclassification of estrogen receptors in teleosts Proc. Natl. Acad. Sci. U. S. A. 97 2000 10751 10756
53. J. Lister Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential Dev. Biol. 237 2001 333 344
54. E.F. Chiang Two sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites Dev. Biol. 231 2001 149 163
55. T. Udono Structural organization of the human microphthalmia-associated transcription factor gene containing four alternative promoters Biochim. Biophys. Acta 1491 2000 205 219
56. J. Kent A male-specific role for SOX9 in vertebrate sex determination Development 122 1996 2813 2822
57. M.P. Matise, and A.L. Joyner Expression patterns of developmental control genes in normal and Engrailed-1 mutant mouse spinal cord reveal early diversity in developing interneurons J. Neurosci. 17 1997 7805 7816
58. B. Feldman Zebrafish organizer development and germ-layer formation require nodal-related signals Nature 395 1998 181 185
59. S. Nornes Zebrafish contains two Pax6 genes involved in eye development Mech. Dev. 77 1998 185 196
60. P.L. Pfeffer Characterization of three novel members of the zebrafish Pax2/5/8 family: Dependency of Pax5 and Pax8 expression on the Pax2.1 (noi) function Development 125 1998 3063 3074
61. M.R. Rebagliati cyclops encodes a nodal-related factor involved in midline signaling Proc. Natl. Acad. Sci. U. S. A. 95 1998 9932 9937
62. A.C. Oates Gene duplication of zebrafish JAK2 homologs is accompanied by divergent embryonic expression patterns; only jak2a is expressed during erythropoiesis Dev. Dyn. 215 1999 352 370
63. S. De Martino Expression of sox11 gene duplicates in zebrafish suggests the reciprocal loss of ancestral gene expression patterns in development Dev. Dyn. 217 2000 279 292
64. A.E. Bruce Additional hox clusters in the zebrafish: divergent expression patterns belie equivalent activities of duplicate hoxB5 genes Evol. Dev. 3 2001 127 144
65. E.F. Chiang Two Cyp19 (P450 aromatase) genes on duplicated zebrafish chromosomes are expressed in ovary or brain Mol. Biol. Evol. 18 2001 542 550
66. A. Locascio Modularity and reshuffling of Snail and Slug expression during vertebrate evolution Proc. Natl. Acad. Sci. U. S. A. 99 2002 16841 16846
67. J.M. McClintock Knockdown of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention Development 129 2002 2339 2354
68. W.A. Cresko Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish Dev. Dyn. 228 2003 480 489
69. C. Jozefowicz The fates of zebrafish Hox gene duplicates J. Struct. Funct. Genomics 3 2003 185 194
70. K. Okubo A novel third gonadotropin-releasing hormone receptor in the medaka Oryzias latipes: evolutionary and functional implications Gene 314 2003 121 131
71. K. Yasumoto A big gene linked to small eyes encodes multiple Mitf isoforms: many promoters make light work Pigment Cell Res. 11 1998 329 336
72. H. Pöpperl Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx Cell 81 1995 1031 1042
73. J.S. Taylor Genome duplication, divergent resolution and speciation Trends Genet. 17 2001 299 301
74. M. Lynch, and A. Force The origin of interspecific genomic incompatibility via gene duplication Am. Nat. 156 2000 590 605
75. J.S. McKinnon Evidence for ecology's role in speciation Nature 429 2004 294 298
76. M. Kishida, and G.V. Callard Distinct cytochrome P450 aromatase isoforms in zebrafish (Danio rerio) brain and ovary are differentially programmed and estrogen regulated during early development Endocrinology 142 2001 740 750
77. J. Wittbrodt Medaka - a model organism from the Far East Nat. Rev. Genet. 3 2002 53 64
78. M.S. Clark Use of the Japanese pufferfish (Fugu rubripes) in comparative genomics Mar. Biotechnol (NY) 3 2001 S130 S140
79. S. Aparicio Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes Proc. Natl. Acad. Sci. U. S. A. 92 1995 1684 1688
80. S. Schwartz MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences Nucleic Acids Res. 31 2003 3518 3524
81. C. Mayor VISTA: visualizing global DNA sequence alignments of arbitrary length Bioinformatics 16 2000 1046 1047
82. A.L. Joyner, and M. Hanks The engrailed genes: Evolution of function Sem. Dev. Biol. 2 1991 435 445
83. I. Varlet Nodal expression in the primitive endoderm is required for specification of the anterior axis during mouse gastrulation Development 124 1997 1033 1044
84. P. Blader, and U. Strähle Developmental biology: casting an eye over cyclopia Nature 395 1998 112 113
85. K. Sampath Induction of the zebrafish ventral brain and floorplate requires cyclops/nodal signalling Nature 395 1998 185 189
86. S.T. Dougan The role of the zebrafish nodal-related genes squint and cyclops in patterning of mesendoderm Development 130 2003 1837 1851
87. R.F. Spokony The transcription factor Sox9 is required for cranial neural crest development in Xenopus Development 129 2002 421 432
88. Y. Mori-Akiyama Sox9 is required for determination of the chondrogenic cell lineage in the cranial neural crest Proc. Natl. Acad. Sci. U. S. A. 100 2003 9360 9365
89. Y.L. Yan A zebrafish sox9 gene required for cartilage morphogenesis Development 129 2002 5065 5079
90. W. Bi Haploinsufficiency of Sox9 results in defective cartilage primordia and premature skeletal mineralization Proc. Natl. Acad. Sci. U. S. A. 98 2001 6698 6703
91. W. Bi Sox9 is required for cartilage formation Nat. Genet. 22 1999 85 89
92. A. Nasevicius, and S.C. Ekker Effective targeted gene 'knockdown' in zebrafish Nat. Genet. 26 2000 216 220
93. K.A. Urtishak Targeted gene knockdown in zebrafish using negatively charged peptide nucleic acid mimics Dev. Dyn. 228 2003 405 413
94. M.A. Kuziora, and W. McGinnis Different transcripts of the Drosophila Abd-B gene correlate with distinct genetic sub-functions EMBO J. 7 1988 3233 3244
95. N.M. Mehta Calcitonin for osteoporosis and bone pain Curr. Pharm. Des. 9 2003 2659 2676