Evolution of Hox clusters in salmonidae: A comparative analysis between atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

Journal of Molecular Evolution

Volumn 61, Issue 5, 2005, Pages 636-649

  Moghadam, Hooman K ^a   Ferguson, Moira M ^a   Danzmann, Roy G ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

Atlantic salmon; Genetic map; Hox genes; Salmonid

Indexed keywords

ARTICLE; ATLANTIC SALMON; CLUSTER ANALYSIS; COMPARATIVE STUDY; EVOLUTION; FISH; GENE CLUSTER; GENE DUPLICATION; GENE IDENTIFICATION; GENE LOCATION; GENETIC LINKAGE; GENETIC ORGANIZATION; GENETICS; GENOMICS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; ORYZIAS; PHYLOGENY; PUFFER FISH; RAINBOW TROUT; SALMONID; SEQUENCE HOMOLOGY; TELEOST; ZEBRA FISH;

ANIMALS; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENOME; HOMEODOMAIN PROTEINS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEOTIDES; ONCORHYNCHUS KISUTCH; PHYLOGENY; SALMO SALAR;

DANIO RERIO; ONCORHYNCHUS MYKISS; ORYZIAS; ORYZIAS LATIPES; SALMO SALAR; SALMONIDAE; SPHOEROIDES NEPHELUS; TAKIFUGU RUBRIPES; TELEOSTEI; TETRAODONTIDAE;

EID: 27744588853     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0338-7     Document Type: Article

References (52)

1. Allendorf FW, Danzmann RG (1997) Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout. Genetics 145:1083-1092
2. Allendorf FW, Thorgaard GH (1984) Tetraploidy and the evolution of salmonid fishes. In: Turner JB (ed) Evolutionary genetics of fishes. Plenum Press, New York, pp 1-53
3. Amores A, Force A, Yan YL, Loly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, Westerfield M, Ekker M, Postlethwait JH (1998) Zebrafish Hox clusters and vertebrate genome evolution. Science 282:1711-1714
4. Amores A, Suzuki T, Yan YL, Pomeroy J, Singer A, Amemiya C, Postlethwait JH (2004) Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res 14:1-10
5. Aparicio S, Hawker K, Cottage A, Mikawa Y, Zuo L, Venkatesh B, Chen E, Krumlauf R, Brenner S (1997) Organization of the Fugu rubripes Hox clusters: Evidence for continuing evolution of vertebrate Hox complexes. Nat Genet 16:79-83
6. Bhattacharya D, Aubry J, Twait EC, Jurk S (2000) Actin gene duplication and the evolution of morphological complexity in land plants. J Phycol 36:813-820
7. Bürglin TR (1994) A comprehensive classification of homeobox genes. In: Deboule D (ed) Guidebook to the homeobox genes. Oxford University Press, Oxford, pp 25-72
8. de Rosa R, Grenier JK, Andreevas T, Cook CE, Adoutte A, Akam M, Carroll SB, Balavoine G (1999) Hox genes in brachiopods and priapulids and protostome evolution. Nature 399:772-776
9. Ferrier DE, Akam M (1996) Organization of the Hox gene cluster in the grasshopper, Schistocerca gregaria. Proc Natl Acad Sci USA 93:13024-13029
10. Ferrier DE, Minguillon C, Holland PW, Garcia-Fernàndez J (2000) The amphioxus Hox cluster: Deuterostome posterior flexibility and Hox14. Evol Dev 2:284-293
11. Ferrier DE (2004) Hox genes: Did the vertebrate ancestor have a Hox14? Curr Biol 14:210-211
12. Force A, Amores A, Postlethwait JH (2002) Hox cluster organization in the jawless vertebrate Petromyzon marinus. J Exp Zool 294:30-46
13. Garcia-Fernàndez J, Holland PWH (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370:563-566
14. Hartley SE (1987) The chromosomes of salmonid fishes. Biol Rev 62:197-214
15. Hasebe M (1999) Evolution of reproductive organs in land plants. J Plant Res 112:463-474
16. Ishiguro NB, Miya M, Nishida M (2003) Basal euteleostean relationships: A mitogenomic perspective on the phylogenetic reality of the " Protacanthopterygii." Mol Phylogenet Evol 27:476-488
17. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinlca M, Vagherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957
18. Johnson KR, Wright JEJ, May B (1987) Linkage relationships reflecting ancestral tetraploidy in salmonid fish. Genetics 116:579-591
19. Krumlauf R (1994) Hox genes in vertebrate development. Cell 78:191-201
20. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245
21. Lewis EB (1992) The 1991 Albert Lasker Medical Awards. Clusters of master control genes regulate the development of higher organisms. JAMA 267:1524-1531
22. Longhurst TJ, Joss JMP (1999) Homeobox genes in the Australian lungfish, Neoceratodus forsteri. J Exp Zool 285:140-145
23. Lynch M, Conery JS (2003) The evolutionary demography of duplicate genes. J Struct Funct Genomics 3:35-44
24. Málaga-Trillo E, Meyer A (2001) Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Am Zool 41:676-686
25. Martinez P, Rast JP, Arenas-Mena C, Davidson EH (1999) Organization of an echinoderm Hox gene cluster. Proc Natl Acad Sci USA 96:1469-1474
26. McGinnis W (1994) A century of homeosis, a decade of homeoboxes. Genetics 137:607-611
27. McGinnis W, Krumlauf R (1992) Homeobox genes and axial patterning. Cell 137:283-302
28. McGinnis W, Hart CP, Gehring WJ, Ruddle FH (1984) Molecular cloning and chromosome mapping of a mouse DNA sequence homologous to homeotic genes of Drosophila. Cell 38:675-680
29. Moghadam HK, Ferguson MM, Danzmann RG (2005) Evidence for Hox gene duplication in rainbow trout (Oncorhynchus mykiss): A tetraploid model species. J Mol Evol 61:(in press)
30. Morgenstern B (1999) DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15:211-218
31. Naruse K, Fulcamachi S, Mitani H, Kondo M, Matsuoka T, Kondo S, Hanamura N, Morita Y, Hasegawa K, Nishigaki R, Shimada A, Wada H, Kusakabe T, Suzuki N, Kinoshita M, Kanamori A, Terado T, Kimura H, Nonaka M, Shima A (2000) A detailed linkage map of medaka, Oryzias latipes: Comparative genomics and genome evolution. Genetics 154:1773-1784
32. Naruse K, Tanaka M, Mita K, Shima A, Postlethwait J, Mitani H (2004) A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res 14:820-828
33. Nelson JS (1994) Fishes of the world. John Wiley and Sons, New York
34. Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH (2003) A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 34:102-115
35. Ohno S (1970) Evolution by gene duplication. Springer Verlag, New York
36. Phillips RB, Rab P (2001) Chromosome evolution in the Salmonidae (Pisces): An update. Biol Rev Camb Philos Soc 76:1-25
37. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS (2000) Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10:1890-1902
38. Prince VE, Joly L, Ekker M, Ho RK (1998) Zebrafish Hox genes: Genomic organization and modified colinear expression patterns in the trunk. Development 125:407-420
39. Ruddle FH, Bartels JL, Bentley KL, Kappen C, Murtha MT, Pendleton JW (1994) Evolution of Hox genes. Annu Rev Genet 28:423-442
40. Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, Khoo SK, Woram RA, Okamoto N, Ferguson MM, Holm LE, Guyomard R, Hoyheim B (2000) A micro satellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex specific differences in recombination rates. Genetics 155:1331-1345
41. Schughart K, Kappen C, Ruddle FH (1989) Duplication of large genomic regions during the evolution of vertebrate homeobox genes. Proc Natl Acad Sci USA 86:7067-7071
42. Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D (2004) Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 431:67-71
43. Sidow A (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6:715-722
44. Stellwag EJ (1999) Hox gene duplication in fish. Semin Cell Dev Biol 10:531-540
45. Taylor JS, Van de Peer Y, Braasch I, Meyer A (2001) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci 356:1661-1679
46. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y (2003) Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res 13:382-390
47. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTALX Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
48. Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y (2004) 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 USA 101:1638-1643
49. Wittbrodt J, Meyer A, Schartl M (1998) More genes in fish. Bio-Essay 20:511-515
50. Woram RA, McGowan C, Stout JA, Gharbi K, Ferguson MM, Hoyheim B, Davidson EA, Davidson WS, Rexroad C, Danzmann RG (2004) A genetic linkage map for Arctic char (Salvelinus alpinus): Evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents. Genome 47:304-315
51. Wright JEJ, Johnson K, Hollister A, May B (1983) Meiotic models to explain classical linkage, pseudolinkage, and chromosome pairing in tetraploid derivative salmonid genomes. Isozymes Curr Top Biol Med Res 10:239-260
52. Zhang J, Nei M (1996) Evolution of Antennapedia class homeobox genes. Genetics 142:295-303