Regulatory evolution of a duplicated heterodimer across species and tissues of allopolyploid clawed frogs (Xenopus)

Journal of Molecular Evolution

Volumn 68, Issue 3, 2009, Pages 236-247

  Anderson, Dave W ^a   Evans, Ben J ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Allopolyploidization; Cis Regulation; Expression divergence; Gene duplication; Pseudogenization; Trans Regulation

Indexed keywords

ANIMALS; BONE MARROW; BRAIN; DATA INTERPRETATION, STATISTICAL; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENES, RAG-1; LIVER; MODELS, GENETIC; MULTIPROTEIN COMPLEXES; MYOCARDIUM; PHYLOGENY; POLYPLOIDY; REGULATORY ELEMENTS, TRANSCRIPTIONAL; UP-REGULATION; XENOPUS; XENOPUS PROTEINS;

XENOPUS (GENUS); XENOPUS LAEVIS;

EID: 62949219651     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9197-6     Document Type: Article

References (38)

1. KL Adams R Cronn R Percifeld JF Wendel 2003 Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing Proc Natl Acad Sci USA 100 4649
2. W Albertin T Balliau P Brabant A-M Chévre F Eber C Malosse H Thiellement 2006 Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids Genetics 173 1101 1113
3. CH Bassing W Swat FW Alt 2002 The mechanism and regulation of chromosomal V(D)J recombination Cell 109 S45 S55
4. RB Brem G Yvert R Clinton L Kruglyak 2002 Genetic dissection of transcriptional regulation in budding yeast Science 296 752 755
5. CI Castillo-Davis DL Hartl G Achaz 2004 cis-regulatory and protein evolution in orthologous and duplicate genes Genome Res 14 1530 1536
6. FJJ Chain BJ Evans 2006 Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis PLoS Genetics 2 e56
7. FJJ Chain D Ilieva BJ Evans 2008 Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization BMC Evol Biol 8 43
8. CR Cowles JN Hirschhorn D Altshuler ES Lander 2002 Detection of regulatory variation in mouse genes Nat Genet 32 432 437
9. DR Denver K Morris JT Streelman SK Kim M Lynch WK Thoman 2005 The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans Nature Genet 37 544 548
10. BJ Evans 2007 Ancestry influences the fate of duplicated genes millions of years after duplication in allopolyploid clawed frogs (Xenopus) Genetics 176 1119 1130
11. Evans BJ (2008) Genome evolution and speciation genetics of allopolyploid clawed frogs (Xenopus and Silurana). Frontiers Biosci 4687-4706
12. BJ Evans DB Kelley RC Tinsley DJ Melnick DC Cannatella 2004 A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution Mol Phylogen Evol 33 197 213
13. BJ Evans DB Kelley DJ Melnick DC Cannatella 2005 Evolution of RAG-1 in polyploid clawed frogs Mol Biol Evol 22 1193 1207
14. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
15. A Force M Lynch B Pickett A Amores YL Yan JH Postlethwait 1999 Preservation of duplicate genes by complementary, degenerative mutations Genetics 151 1531 1545
16. P Greenhalgh CEM Olesen LA Steiner 1993 Characterization and expression of recombination activating genes (RAG-1 and RAG-2) in Xenopus laevis J Immunol 151 3100 3110
17. JP Huelsenbeck F Ronquist 2001 MrBayes: Bayesian inference of phylogenetic trees Bioinformatics 17 754 755
18. IK Jordan L Marino-Ramirez EV Koonin 2005 Evolutionary significance of gene expression divergence Gene 345 119 126
19. M Kirst CJ Basten AA Myburg ZB Zeng RR Seberoff 2005 Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid Genetics 169 2295 2303
20. KE Kruckeberg SN Thibodeau 2004 Pyrosequencing technology as a method for the diagnosis of multiple endocrine neoplasia type 2 Clin Chem 50 522 529
21. CR Landry PJ Wittkopp CH Taubes JM Ranz AG Clark DL Hartl 2005 Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila Genetics 171 1813 1822
22. B Lemos CD Meiklejohn DL Hartl 2004 Regulatory evolution across the protein interaction network Nature Genet 36 1059 1060
23. B Lemos CD Meiklejohn M Cáceres DL Hartl 2005 Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories Evolution 59 126 137
24. MZ Ludwig C Bergman NH Patel M Kreitman 2000 Evidence for stabilizing selection in a eukaryotic enhancer element Nature 403 564 567
25. M Lynch A Force 2000 The probability of duplicate gene preservation by subfunctionalization Genetics 154 459 473
26. M Morley CM Molony TM Weber JL Devlin KG Ewens RS Spielman VG Cheung 2004 Genetic analysis of genome-wide variation in human gene expression Nature 430 743 747
27. TK Nilsson CA Johansson 2004 A novel method for diagnosis of adult hypolactasia by genotyping of the -13910 C/T polymorphism with Pyrosequencing technology Scand J Gastroenterol 39 287 290
28. CL Organ AM Shedlock A Meade M Pagel SV Edwards 2007 Origin of avian genome size and structure in non-avian dinosaurs Nature 446 180 184
29. M Pagel 1997 Inferring evolutionary processes from phylogenies Zoologica Scripta 26 331 348
30. M Pagel 1999 Inferring the historical patterns of biological evolution Nature 401 877 884
31. WR Rice 1989 Analyzing tables of statistical tests Evolution 43 223 225
32. S Spicuglia DM Franchini P Ferrier 2006 Regulation of V(D)J recombination Curr Opin Immunol 18 158 163
33. C Venditti A Meade M Pagel 2006 Detecting the node-density artifact in phylogeny reconstruction Syst Biol 55 637 643
34. J Wang L Tian H-S Lee NE Wei H Jiang B Watson A Madlung TC Osborn RW Doerge L Comai ZJ Chen 2006 Genomewide nonadditive gene regulation in Arabidopsis allotetraploids Genetics 172 507 517
35. PJ Wittkopp BK Haerum AG Clark 2004 Evolutionary changes in cis and trans gene regulation Nature 430 85 88
36. PJ Wittkopp BK Haerum AG Clark 2008 Regulatory changes underlying expression differences within and between Drosophila species Nature Genet 40 346 350
37. H Yan W Yuan VE Velculescu B Vogelstein KW Kinzler 2002 Allelic variation in human gene expression Science 297 1143
38. G Yvert RB Brem J Whittle JM Akey E Foss EN Smith R Mackelprang L Kruglyak 2003 Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors Nature Genet 35 57 64