Comparative genome mapping reveals evidence of gene conversion between Sox9 paralogs of rainbow trout (Oncorhynchus mykiss)

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 4, Issue 3, 2009, Pages 147-153

  Alfaqih, Mahmoud A ^a,b   Steele, Craig A ^c   Morris, Robert T ^a   Thorgaard, Gary H ^c  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b MUTAH UNIVERSITY   (Jordan)

^c Center for Reproductive Biology   (United States)

Author keywords

Gene conversion; Genetic map; Paralogs; Polyploid; Pseudo linkage; Rainbow trout; Salmonids; Teleost

Indexed keywords

TRANSCRIPTION FACTOR SOX9;

3' UNTRANSLATED REGION; ARTICLE; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; GENE CONSTRUCT; GENE CONVERSION; GENE DUPLICATION; GENE LOCUS; GENETIC RECOMBINATION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PARALOGY; PHYLOGENY; PRIORITY JOURNAL; RAINBOW TROUT; TELEOST;

ONCORHYNCHUS MYKISS; SALMONIDAE; TELEOSTEI;

EID: 67650165673     PISSN: 1744117X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbd.2009.01.003     Document Type: Article

References (56)

1. Allendorf F.W., and Danzmann R.G. Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout. Genetics 145 (1997) 1083-1092
2. Allendorf F.W., and Thorgaard G.H. Tetraploidy and the evolution of salmonid fishes. The Evolutionary Genetics of Fishes (1984), Plenum publishing, New York
3. Amores A., Force A., Yan Y.L., Joly L., Amemiya C., Fritz A., Ho R.K., Langeland J., Prince V., Wang Y.L., Westerfield M., Ekker M., and Postlethwait J.H. Zebrafish hox clusters and vertebrate genome evolution. Science 282 (1998) 1711-1714
4. Arnheim N.N., Krystal M.M., Schmickel R.R., Wilson G.G., Ryder O.O., and Zimmer E.E. Molecular evidence for genetic exchanges among ribosomal genes on nonhomologous chromosomes in man and apes. Proc. Natl. Acad. Sci. U. S. A. 77 (1980) 7323-7327
5. Baron D., Houlgatte R., Fostier A., and Guiguen Y. Large-scale temporal gene expression profiling during gonadal differentiation and early gametogenesis in rainbow trout. Biol. Reprod. 73 (2005) 959-966
6. Bi W., Deng J.M., Zhang Z., Behringer R.R., and de Crombrugghe B. Sox9 is required for cartilage formation. Nat. Genet. 22 (1999) 85-89
7. Boni M.F., Posada D., and Feldman M.W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176 (2007) 1035-1047
8. Chiang E.F., Pai C.I., Wyatt M., Yan Y.L., Postlethwait J., and Chung B. Two Sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites. Dev. Biol. 231 (2001) 149-163
9. Cresko W.A., Yan Y.L., Baltrus D.A., Amores A., Singer A., Rodriguez-Mari A., and Postlethwait J.H. Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish. Dev. Dyn. 228 (2003) 480-489
10. da Silva S.M., Hacker A., Harley V., Goodfellow P., Swain A., and Lovell-Badge R. Sox9 expression during gonadal development implies a conserved role for the gene in testis differentiation in mammals and birds. Nat. Genet. 14 (1996) 62-68
11. Foster J.W., Dominguez-Steglich M.A., Guioli S., Kowk G., Weller P.A., Stevanovic M., Weissenbach J., Mansour S., Young I.D., Goodfellow P.N., et al. Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene. Nature 372 (1994) 525-530
12. Gharbi K., Gautier A., Danzmann R.G., Gharbi S., Sakamoto T., Hoyheim B., Taggart J.B., Cairney M., Powell R., Krieg F., Okamoto N., Ferguson M.M., Holm L.E., and Guyomard R. A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish. Genetics 172 (2006) 2405-2419
13. Gibbs M.M.J., Armstrong J.J.S., and Gibbs A.A.J. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16 (2000) 573-582
14. Gubbay J., Collignon J., Koopman P., Capel B., Economou A., Munsterberg A., Vivian N., Goodfellow P., and Lovell-Badge R. A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes. Nature 346 (1990) 245-250
15. Guyomard R., Mauger S., Tabet-Canale K., Martineau S., Genet C., Krieg F., and Quillet E. A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 7 (2006) 302
16. Holmes E.E.C., Worobey M.M., and Rambaut A.A. Phylogenetic evidence for recombination in dengue virus. Mol. Biol. Evol. 16 (1999) 405-409
17. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
18. Hughes A.L., and Friedman R. 2R or not 2R: testing hypotheses of genome duplication in early vertebrates. J. Struct. Funct. Genomics. 3 (2003) 85-93
19. Johnson K.R., Wright Jr. J.E., and May B. Linkage relationships reflecting ancestral tetraploidy in salmonid fish. Genetics 116 (1987) 579-591
20. Kent J., Wheatley S.C., Andrews J.E., Sinclair A.H., and Koopman P. A male-specific role for Sox9 in vertebrate sex determination. Development 122 (1996) 2813-2822
21. Kluver N., Kondo M., Herpin A., Mitani H., and Schartl M. Divergent expression patterns of Sox9 duplicates in teleosts indicate a lineage specific subfunctionalization. Dev. Genes. Evol. 215 (2005) 297-305
22. Koopman P., Schepers G., Brenner S., and Venkatesh B. Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes. Gene 328 (2004) 177-186
23. Lander E.S., Green P., Abrahamson J., Barlow A., Daly M.J., Lincoln S.E., and Newburg L. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1 (1987) 174-181
24. Leigh Brown A.A.J., and Ish-Horowicz D.D. Evolution of the 87A and 87C heat-shock loci in Drosophila. Nature 290 (1981) 677-682
25. Martin D., and Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 16 (2000) 562-563
26. Martin D.D.P., Posada D.D., Crandall K.K.A., and Williamson C.C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum. Retrovir. 21 (2005) 98-102
27. Martin D.P., Williamson C., and Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21 (2005) 260-262
28. Meyer A., and 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. 11 (1999) 699-704
29. Moghadam H.K., Ferguson M.M., and Danzmann R.G. Evidence for Hox gene duplication in rainbow trout (Oncorhynchus mykiss): a tetraploid model species. J. Mol. Evol. 61 (2005) 804-818
30. Morrish B.C., and Sinclair A.H. Vertebrate sex determination: many means to an end. Reproduction 124 (2002) 447-457
31. Naruse K., Tanaka M., Mita K., Shima A., Postlethwait J., and Mitani H. A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res. 14 (2004) 820-828
32. Nelson J.S. Fishes of the World (1994), John Wiley and Sons, New York
33. Nichols K.M., Young W.P., Danzmann R.G., Robison B.D., Rexroad C., Noakes M., Phillips R.B., Bentzen P., Spies I., Knudsen K., Allendorf F.W., Cunningham B.M., Brunelli J., Zhang H., Ristow S., Drew R., Brown K.H., Wheeler P.A., and Thorgaard G.H. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim. Genet. 34 (2003) 102-115
34. Ohno S. Evolution by Gene Duplication (1970), Springer Verlag, New York
35. Ohno S., Wolf U., and Atkin N.B. Evolution from fish to mammals by gene duplication. Hereditas 59 (1968) 169-187
36. Padidam M., Sawyer S., and Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 265 (1999) 218-225
37. Phillips R., and Rab P. Chromosome evolution in the Salmonidae (Pisces): an update. Biol. Revs. 76 (2001) 1-25
38. Phillips R.B., Nichols K.M., DeKoning J.J., Morasch M.R., Keatley K.A., Rexroad III C., Gahr S.A., Danzmann R.G., Drew R.E., and Thorgaard G.H. Assignment of rainbow trout linkage groups to specific chromosomes. Genetics 174 (2006) 1661-1670
39. Posada D., and Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. 98 (2001) 13757-13762
40. Posada D.D., and Crandall K.A. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54 (2002) 396-402
41. Posada D., Crandall K.A., and Holmes E.C. Recombination in evolutionary genomics. Annu. Rev. Genet. 36 (2002) 75-97
42. Postlethwait J.H., Woods I.G., Ngo-Hazelett P., Yan Y.L., Kelly P.D., Chu F., Huang H., Hill-Force A., and Talbot W.S. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10 (2000) 1890-1902
43. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
44. Scott A.F., Heath P., Trusko S., Boyer S.H., Prass W., Goodman M., Czelusniak J., Chang L.Y., and Slightom J.L. The sequence of the gorilla fetal globin genes: evidence for multiple gene conversions in human evolution. Mol. Biol. Evol. 1 (1984) 371-389
45. Sidow A. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6 (1996) 715-722
46. Smith J.M. Analyzing the mosaic structure of genes. J. Mol. Evol. 34 (1992) 126-129
47. Takamatsu N., Kanda H., Ito M., Yamashita A., Yamashita S., and Shiba T. Rainbow trout SOX9: cDNA cloning, gene structure and expression. Gene 202 (1997) 167-170
48. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
49. Vandepoele K., De Vos W., Taylor J.S., Meyer A., and Van de Peer Y. 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
50. Wagner T., Wirth J., Meyer J., Zabel B., Held M., Zimmer J., Pasantes J., Bricarelli F.D., Keutel J., Hustert E., et al. Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene Sox9. Cell 79 (1994) 1111-1120
51. Western P.S., Harry J.L., Graves J.A., and Sinclair A.H. Temperature-dependent sex determination in the American alligator: AMH precedes Sox9 expression. Dev. Dyn. 216 (1999) 411-419
52. Wright Jr. J.E., Johnson K., Hollister A., and May B. Meiotic models to explain classical linkage, pseudolinkage, and chromosome pairing in tetraploid derivative salmonid genomes. Isozymes Curr. Top. Biol. Med. Res. 10 (1983) 239-260
53. Yan Y.L., Miller C.T., Nissen R.M., Singer A., Liu D., Kirn A., Draper B., Willoughby J., Morcos P.A., Amsterdam A., Chung B.C., Westerfield M., Haffter P., Hopkins N., Kimmel C., and Postlethwait J.H. A zebrafish Sox9 gene required for cartilage morphogenesis. Development 129 (2002) 5065-5079
54. Young W.P., Wheleer P.A., Fields R.D., and Thorgaard G.H. DNA fingerprinting confirms isogenecity of androgenetically derived rainbow trout lines. J. Hered. 87 (1996) 77-81
55. Zhou R., Liu L., Guo Y., Yu H., Cheng H., Huang X., Tiersch T.R., and Berta P. Similar gene structure of two Sox9a genes and their expression patterns during gonadal differentiation in a teleost fish, rice field eel (Monopterus albus). Mol. Reprod. Dev. 66 (2003) 211-217
56. Zimmerman A.M., Evenhuis J.P., Thorgaard G.H., and Ristow S.S. A single major chromosomal region controls natural killer cell-like activity in rainbow trout. Immunogenetics 55 (2004) 825-835