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Phylogenetic Analysis of Ciona intestinalis Gene Superfamilies Supports the Hypothesis of Successive Gene Expansions

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Abstract

Understanding the formation of metazoan multigene families is a good approach to reconstitute the evolution of the chordate genome. In this attempt, the analysis of the genome of selected species provides valuable information. Ciona intestinalis belongs to the urochordates, whose lineage separated from the chordate lineage that later gave birth to vertebrates. We have searched available sequences from the small marine ascidian C. intestinalis for orthologs of members of five vertebrate superfamilies, including tyrosine kinase receptors, ETS, FOX and SOX transcription factors, and WNT secreted regulatory factors, and conducted phylogenetic analyses. We have found that most vertebrate subfamilies have a single C. intestinalis ortholog. Our results support the hypothesis of a gene expansion prior the base of chordate ancestry followed by another gene expansion during vertebrate evolution. They also indicate that Ciona intestinalis genome will be a very valuable tool for evolutionary analyses.

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References

  1. L Abi-Rached A Gilles T Shiina P Pontarotti H Inoko (2002) ArticleTitleEvidence for en bloc duplication in vertebrate genomes. Nat Genet 31 100–105 Occurrence Handle10.1038/ng855 Occurrence Handle1:CAS:528:DC%2BD38Xjt1Kgu7k%3D Occurrence Handle11967531

    Article  CAS  PubMed  Google Scholar 

  2. MD Adams SE Celniker RA Holt et al. (2001) ArticleTitleThe genome sequence of Drosophila melanogaster. Science 287 2185–2195 Occurrence Handle10.1126/science.287.5461.2185

    Article  Google Scholar 

  3. F Agnès MM Toux C André F Galibert (1997) ArticleTitleGenomic organization of the extracellular coding region of the human FGFR4 and FLT4 genes: Evolution of the genes encoding receptor tyrosine kinases with immunoglobulin-like domains. J Mol Evol 45 43–49 Occurrence Handle9211733

    PubMed  Google Scholar 

  4. SF Altschul TL Madden AA Schäffer Z Zhang W Miller DJ Lipman (1997) ArticleTitleGapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25 3389–3402 Occurrence Handle9254694

    PubMed  Google Scholar 

  5. A Amores A Force YL Yan L Joly C Amemiya A Fritz R Ho J Langeland V Prince YL Wang M Westerfield M Ekker JM Postlethwait (1998) ArticleTitleZebrafish hox clusters and vertebrate genome evolution. Science 282 1711–1714 Occurrence Handle1:CAS:528:DyaK1cXnslGgtrY%3D Occurrence Handle9831563

    CAS  PubMed  Google Scholar 

  6. S Aparicio (2000) ArticleTitleVertebrate evolution: recent perspectives from fish. Trends Genet 16 54–56 Occurrence Handle10.1016/S0168-9525(99)01934-4 Occurrence Handle1:CAS:528:DC%2BD3cXpsFGrtQ%3D%3D Occurrence Handle10652527

    Article  CAS  PubMed  Google Scholar 

  7. D Birnbaum MJ Pébusque J Imbert A Dib O deLapeyrière F Coulier (1994) ArticleTitleOncogenesis and genome duplication maps. Oncology Rep 1 477–480 Occurrence Handle1:CAS:528:DyaK2cXmsFanu7s%3D

    CAS  Google Scholar 

  8. J Bowles G Schepers P Koopman (2000) ArticleTitlePhylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol 227 239–255 Occurrence Handle10.1006/dbio.2000.9883 Occurrence Handle1:CAS:528:DC%2BD3cXnvVelu7g%3D Occurrence Handle11071752

    Article  CAS  PubMed  Google Scholar 

  9. NM Brooke J Garcia-Fernandez PW Holland (1998) ArticleTitleThe ParaHox gene cluster is an evolutionary sister of the Hox cluster. Nature 392 920–922 Occurrence Handle10.1038/31933 Occurrence Handle1:CAS:528:DyaK1cXjtV2ju7w%3D Occurrence Handle9582071

    Article  CAS  PubMed  Google Scholar 

  10. C Burge S Karlin (1997) ArticleTitlePrediction of complete gene structures in human genomic DNA. J Mol Biol 268 78–94 Occurrence Handle10.1006/jmbi.1997.0951 Occurrence Handle1:CAS:528:DyaK2sXjtlSqtL4%3D Occurrence Handle9149143

    Article  CAS  PubMed  Google Scholar 

  11. J Cooke M Nowak M Boerlijst J Maynard-Smith (1997) ArticleTitleEvolutionary origins and maintenance of redundant gene expression during metaozoan development. Trends Genet 13 360–364 Occurrence Handle1:CAS:528:DyaK2sXlslyjt70%3D Occurrence Handle9287491

    CAS  PubMed  Google Scholar 

  12. F Coulier S Burtey M Chaffanet F Birg D Birnbaum (2000a) ArticleTitleAncestrally-duplicated paraHOX gene clusters in humans. Int J Oncol 17 439–444 Occurrence Handle1:CAS:528:DC%2BD3cXlvFektb4%3D

    CAS  Google Scholar 

  13. F Coulier C Popovici R Villet D Birnbaum (2000b) ArticleTitleMetaHOX gene clusters. J Exp Zool 288 345–351 Occurrence Handle1:CAS:528:DC%2BD3cXovF2rtbs%3D

    CAS  Google Scholar 

  14. P Dehal et al. (2002) ArticleTitleThe draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298 2157–2167 Occurrence Handle10.1126/science.1080049 Occurrence Handle1:CAS:528:DC%2BD38XpsVSkt7o%3D Occurrence Handle12481130

    Article  CAS  PubMed  Google Scholar 

  15. G de Luca di Roseto G Bucciarelli G Bernardi (2002) ArticleTitleAn analysis of the genome of Ciona intestinalis. Gene 295 311–316 Occurrence Handle10.1016/S0378-1119(02)00734-5 Occurrence Handle1:CAS:528:DC%2BD38XntFyqtbo%3D Occurrence Handle12354666

    Article  CAS  PubMed  Google Scholar 

  16. P Duchek K Somogyi G Jekely S Beccari P Rorth (2001) ArticleTitleGuidance of cell migration by the Drosophila PDGF/VEGF receptor. Cell 107 17–26 Occurrence Handle1:CAS:528:DC%2BD3MXnsFOntL8%3D

    CAS  Google Scholar 

  17. N Eldredge SJ Gould (1972) Punctuated equilibria: An alternative to phyletic gradualism. TJM Schopf (Eds) Models of paleobiology. Freeman & Cooper San Francisco 82–115

    Google Scholar 

  18. J Felsenstein (1985) ArticleTitleConfidence-limits on phylogenies—An approach using the bootstrap. Evolution 39 783–791

    Google Scholar 

  19. DEK Ferrier PWH Holland (2002) ArticleTitle Ciona intestinalis ParaHox genes: Evolution of Hox/ParaHox cluster integrity, developmental mode, and temporal colinearity. Mol Phylogenet Evol 24 412–417 Occurrence Handle10.1016/S1055-7903(02)00204-X Occurrence Handle1:CAS:528:DC%2BD38Xms1GgtrY%3D Occurrence Handle12220984

    Article  CAS  PubMed  Google Scholar 

  20. W Fitch (1970) ArticleTitleDistinguishing homologous from analogous proteins. Syst Zool 19 99–113 Occurrence Handle1:CAS:528:DyaE3MXkvFyisw%3D%3D Occurrence Handle5449325

    CAS  PubMed  Google Scholar 

  21. A Force M Lynch FB Pickett A Amores YL Van J Postlethwait (1999) ArticleTitlePreservation of duplicate genes by complementary, degenerative mutations. Genetics 151 1531–1534 Occurrence Handle1:CAS:528:DyaK1MXisV2rs7o%3D Occurrence Handle10101175

    CAS  PubMed  Google Scholar 

  22. R Friedman AL Hughes (2001) ArticleTitlePattern and timing of gene duplication in animal genomes. Genome Res 11 1842–1847 Occurrence Handle10.1101/gr.155801 Occurrence Handle1:CAS:528:DC%2BD3MXotlajuro%3D Occurrence Handle11691848

    Article  CAS  PubMed  Google Scholar 

  23. R Friedman AL Hughes (2003) ArticleTitleThe temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol Biol Evol 20 154–161 Occurrence Handle10.1093/molbev/msg017 Occurrence Handle1:CAS:528:DC%2BD3sXktlOqtg%3D%3D Occurrence Handle12519918

    Article  CAS  PubMed  Google Scholar 

  24. N Galtier M Gouy C Gautier (1996) ArticleTitleSEAVIEW and PHYLO_WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comp Appl Biosci 12 543–545 Occurrence Handle1:CAS:528:DyaK2sXhtlWktLw%3D

    CAS  Google Scholar 

  25. J Gerhart M Kirschner (1997) Cells, embryos and evolution. Blackwell Science Malden

    Google Scholar 

  26. TJ Gibson J Spring (1999) ArticleTitleEvidence in favour of ancient octaploidy in the vertebrate genome. Biochem Soc Trans 28 259–264

    Google Scholar 

  27. JP Gogarten L Olendzenski (1999) ArticleTitleOrthologs, paralogs and genome comparisons. Curr Opin Genet Dev 9 630–636 Occurrence Handle10.1016/S0959-437X(99)00029-5 Occurrence Handle1:CAS:528:DC%2BD3cXhslOjug%3D%3D Occurrence Handle10607614

    Article  CAS  PubMed  Google Scholar 

  28. A Graham (2000) ArticleTitleThe evolution of the vertebrates—Genes and development. Curr Opin Genet Dev 10 624–628 Occurrence Handle10.1016/S0959-437X(00)00135-0 Occurrence Handle1:CAS:528:DC%2BD3cXovFansrk%3D Occurrence Handle11088012

    Article  CAS  PubMed  Google Scholar 

  29. J Grassot G Mouchiroud G Perrière (2003) ArticleTitleRTKdb: Database of receptor tyrosine kinase. Nucleic Acids Res 31 353–358 Occurrence Handle10.1093/nar/gkg036 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSmt7k%3D Occurrence Handle12520021

    Article  CAS  PubMed  Google Scholar 

  30. SJ Gould N Eldredge (1993) ArticleTitlePunctuated equilibrium comes of age. Nature 366 223–227 Occurrence Handle10.1038/366223a0 Occurrence Handle8232582

    Article  PubMed  Google Scholar 

  31. X Gu Y Wang J Gu (2002) ArticleTitleAge distribution of both human gene families shows significant roles of both large-scale and small-scale duplications in vertebrate evolution. Nat Genet 31 205–209 Occurrence Handle10.1038/ng902 Occurrence Handle1:CAS:528:DC%2BD38XktVKgt7o%3D Occurrence Handle12032571

    Article  CAS  PubMed  Google Scholar 

  32. Z Gu A Cavalcanti FC Chen P Bouman WH Li (2002) ArticleTitleExtent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19 256–262 Occurrence Handle11861885

    PubMed  Google Scholar 

  33. T Heino T Karpanen G Wahlstrom M Pulkinen U Eriksson K Alitalo C Roos (2001) ArticleTitleThe Drosophila VEGF receptor homolog is expressed in hemocytes. Mech Dev 109 69–77 Occurrence Handle10.1016/S0925-4773(01)00510-X Occurrence Handle1:CAS:528:DC%2BD3MXnslWrtbw%3D Occurrence Handle11677054

    Article  CAS  PubMed  Google Scholar 

  34. DM Hillis JJ Bull (1993) ArticleTitleAn empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42 182–192

    Google Scholar 

  35. K Hino Y Satou K Yagi N Satoh (2003) ArticleTitleA genomewide survey of developmentally relevant genes in Ciona intestinalis VI. Genes for Wnt, TGFbeta, hedgehog and JAK/STAT signaling pathways. Dev Genes Evol 213 264–272 Occurrence Handle1:CAS:528:DC%2BD3sXltVWgtrg%3D Occurrence Handle12739142

    CAS  PubMed  Google Scholar 

  36. N Holland J Chen (2001) ArticleTitleOrigin and early evolution of the vertebrates: new insights from advances in molecular biology, anatomy, and palaeontology. BioEssays 23 142–151 Occurrence Handle10.1002/1521-1878(200102)23:2<142::AID-BIES1021>3.0.CO;2-5 Occurrence Handle1:CAS:528:DC%2BD3MXptVOrsrk%3D Occurrence Handle11169587

    Article  CAS  PubMed  Google Scholar 

  37. PWH Holland J Garcia-Fernandez NA Williams A Sidow (1994) ArticleTitleGene duplications and the origins of vertebrate development. Development Suppl 125–133

    Google Scholar 

  38. X Huang A Madan (1999) ArticleTitleCAP3: A DNA sequence assembly program. Genome Res 9 868–877 Occurrence Handle10.1101/gr.9.9.868 Occurrence Handle1:CAS:528:DyaK1MXmslKgs7Y%3D Occurrence Handle10508846

    Article  CAS  PubMed  Google Scholar 

  39. AL Hughes (2002) ArticleTitleAdaptive evolution after gene duplication. Trends Genet 18 433–434 Occurrence Handle10.1016/S0168-9525(02)02755-5 Occurrence Handle1:CAS:528:DC%2BD38Xmtlelt7w%3D Occurrence Handle12175796

    Article  CAS  PubMed  Google Scholar 

  40. AL Hughes J da Silva R Friedman (2001) ArticleTitleAncient genome duplications did not structure the human HOX-bearing chromosomes. Genome Res 11 771–780 Occurrence Handle10.1101/gr.GR-1600R Occurrence Handle1:CAS:528:DC%2BD3MXjs1Wmurs%3D Occurrence Handle11337473

    Article  CAS  PubMed  Google Scholar 

  41. KH Kaestner W Knochel DE Martinez (2000) ArticleTitleA unified nomenclature for the winged helix/forkhead transcription factors. Genes Dev 14 142–146 Occurrence Handle10702024

    PubMed  Google Scholar 

  42. K Katoh T Miyata (1999) ArticleTitleA heuristic approach of maximum likelihood method for inferring phylogenetic tree and an application to the mammalian SOX-3 origin of the testis-determining gene SRY. FEBS Lett 463 129–132 Occurrence Handle1:CAS:528:DyaK1MXnvFems7g%3D Occurrence Handle10601652

    CAS  PubMed  Google Scholar 

  43. FA Kondrashov IB Rogozin YI Wolf EV Koonin (2002) ArticleTitleSelection in the evolution of gene duplications. Genome Biol 3 0008 Occurrence Handle10.1186/gb-2002-3-2-research0008

    Article  Google Scholar 

  44. EV Koonin (2001) ArticleTitleAn apology for orthologs—or brave new memes. Genome Biol 2 1005.1–1005. Occurrence Handle10.1186/gb-2001-2-4-comment1005

    Article  Google Scholar 

  45. ES Lander (2001) ArticleTitleInitial sequencing and analysis of the human genome. Nature 409 860–921 Occurrence Handle1:CAS:528:DC%2BD3MXhsFCjtLc%3D Occurrence Handle11237011

    CAS  PubMed  Google Scholar 

  46. V Laudet C Hanni D Stehelin M Duterque-Coquillaud (1999) ArticleTitleMolecular phylogeny of the ETS family. Oncogene 18 1351–1359 Occurrence Handle1:CAS:528:DyaK1MXhsFaqtLo%3D Occurrence Handle10022817

    CAS  PubMed  Google Scholar 

  47. CJ Lee WI Chan M Cheung YC Cheng VJ Appleby AT Orme PJ Scotting (2002) ArticleTitleCIC, a member of a novel subfamily of the HMG-box superfamily, is transiently expressed in developing granule neurons. Brain Res Mol Brain Res 106 151 Occurrence Handle10.1016/S0169-328X(02)00439-4 Occurrence Handle1:CAS:528:DC%2BD38XnvVOlt7k%3D Occurrence Handle12393275

    Article  CAS  PubMed  Google Scholar 

  48. O Lespinet YI Wolf EV Koonin L Aravind (2002) ArticleTitleThe role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 12 1048–1059

    Google Scholar 

  49. M Leveugle K Prat N Perrier D Birnbaum F Coulier (2003) ArticleTitleParaDB: A tool for paralogy mapping in vertebrate genomes. Nucleic Acids Res 31 63–67 Occurrence Handle10.1093/nar/gkg106 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSnsr4%3D Occurrence Handle12519948

    Article  CAS  PubMed  Google Scholar 

  50. WH Li Z Gu H Wang A Nekrutenko (2001) ArticleTitleEvolutionary analysis of the human genome. Nature 409 847–849 Occurrence Handle1:CAS:528:DC%2BD3MXhsFCjtL4%3D Occurrence Handle11237007

    CAS  PubMed  Google Scholar 

  51. LG Lundin (1993) ArticleTitleEvolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16 1–19 Occurrence Handle10.1006/geno.1993.1133 Occurrence Handle1:CAS:528:DyaK3sXkt1Wnsr4%3D Occurrence Handle8486346

    Article  CAS  PubMed  Google Scholar 

  52. M Lynch JS Conery (2000) ArticleTitleThe evolutionary fate and consequences of duplicate genes. Science 290 1151–1155 Occurrence Handle10.1126/science.290.5494.1151 Occurrence Handle1:CAS:528:DC%2BD3cXotVChsb8%3D Occurrence Handle11073452

    Article  CAS  PubMed  Google Scholar 

  53. W Makalowski (2001) ArticleTitleAre we polyploids? A brief history of one hypothesis. Genome Res 11 667–670 Occurrence Handle10.1101/gr.188801 Occurrence Handle1:CAS:528:DC%2BD3MXjs1Wmtbk%3D Occurrence Handle11337465

    Article  CAS  PubMed  Google Scholar 

  54. A Martin (2001) ArticleTitleIs tetralogy true? Lack of support for the “one-to-four” rule. Mol Biol Evol 18 89–93 Occurrence Handle1:CAS:528:DC%2BD3MXhtVSmsL4%3D Occurrence Handle11141196

    CAS  PubMed  Google Scholar 

  55. F Mazet SM Shimeld (2002) ArticleTitleGene duplication and divergence in the early evolution of vertebrates. Curr Opin Genet Dev 12 393–396 Occurrence Handle10.1016/S0959-437X(02)00315-5 Occurrence Handle1:CAS:528:DC%2BD38XkvF2isb8%3D Occurrence Handle12100882

    Article  CAS  PubMed  Google Scholar 

  56. A McLysaght K Hokamp KH Wolfe (2002) ArticleTitleExtensive genomic duplication during early chordate evolution. Nat Genet 31 200–204 Occurrence Handle10.1038/ng884 Occurrence Handle1:CAS:528:DC%2BD38XktVKgsbc%3D Occurrence Handle12032567

    Article  CAS  PubMed  Google Scholar 

  57. C Minguillon CE Ferrier C Cebrian J Garcia-Fernandez (2002) ArticleTitleGene duplications in the prototypical cephalochordate amphioxus. Gene 287 121–128 Occurrence Handle10.1016/S0378-1119(01)00828-9 Occurrence Handle11992730

    Article  PubMed  Google Scholar 

  58. R Nusse (2001) ArticleTitleAn ancient cluster of Wnt paralogues. Trends Genet 17 443 Occurrence Handle10.1016/S0168-9525(01)02349-6 Occurrence Handle1:STN:280:DC%2BD3MvksF2nsQ%3D%3D

    Article  CAS  Google Scholar 

  59. S Ohno (1970) Evolution by gene duplication. Springer Verlag Berlin/Heidelberg/New York

    Google Scholar 

  60. V Ollendorff MG Mattei E Fournier J Adélaïde M Lopez O Rosnet D Birnbaum (1998) ArticleTitleA third human CBL gene is on chromosome 19. Int J Oncol 13 1159–1161 Occurrence Handle1:CAS:528:DyaK1cXotVajsLs%3D Occurrence Handle9824625

    CAS  PubMed  Google Scholar 

  61. SP Otto P Yong (2002) ArticleTitleThe evolution of gene duplicates. Adv Genet 46 451–483 Occurrence Handle1:CAS:528:DC%2BD38XktVSlsbo%3D Occurrence Handle11931235

    CAS  PubMed  Google Scholar 

  62. RD Page JA Cotton (2002) ArticleTitleVertebrate phylogenomics: Reconciled trees and gene duplications. Pac Symp Biocomput . 536–547

    Google Scholar 

  63. MJ Pébusque F Coulier D Birnbaum P Pontarotti (1998) ArticleTitleAncient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol Biol Evol 15 1145–1159 Occurrence Handle1:CAS:528:DyaK1cXls1Kis7g%3D Occurrence Handle9729879

    CAS  PubMed  Google Scholar 

  64. S Pollard PWH Holland (2000) ArticleTitleEvidence for 14 homeobox gene clusters in human genome ancestry. Curr Biol 10 1059–1062

    Google Scholar 

  65. C Popovici R Roubin F Coulier P Pontarotti D Birnbaum (1999) ArticleTitleThe family of Caenorhabditis elegans tyrosine kinase receptors: Similarities and differences with mammalian receptors. Genome Res 9 1026–1039 Occurrence Handle10.1101/gr.9.11.1026 Occurrence Handle1:CAS:528:DyaK1MXns12ktrw%3D Occurrence Handle10568743

    Article  CAS  PubMed  Google Scholar 

  66. C Popovici M Leveugle D Birnbaum F Coulier (2001a) ArticleTitleHomeobox gene clusters and the human paralogy map. FEBS Lett 491 237–242 Occurrence Handle1:CAS:528:DC%2BD3MXhs1ehs74%3D

    CAS  Google Scholar 

  67. C Popovici M Leveugle D Birnbaum F Coulier (2001b) ArticleTitleCoparalogy; Physical and functional clusterings in the human genome. Biochem Biophys Res Commun 288 362–370 Occurrence Handle1:CAS:528:DC%2BD3MXnsF2qtLk%3D

    CAS  Google Scholar 

  68. O Rosnet D Stephenson MG Mattei S Marchetto M Shibuya VM Chapman D Birnbaum (1993) ArticleTitleClose physical linkage of the FLT1 and FLT3 genes on chromosome 13 in man and chromosome 5 in mouse. Oncogene 8 173–179 Occurrence Handle1:CAS:528:DyaK3sXitVKmu7s%3D Occurrence Handle8380915

    CAS  PubMed  Google Scholar 

  69. Y Satou K Imai N Satoh (2002) ArticleTitleFgf genes in the basal chordate Ciona intestinalis. Dev Genes Evol 212 432–438 Occurrence Handle10.1007/s00427-002-0266-8 Occurrence Handle1:CAS:528:DC%2BD38XpsV2msrw%3D Occurrence Handle12373588

    Article  CAS  PubMed  Google Scholar 

  70. Y Satou Y Sasakura L Yamada KS Imai N Satoh B Degnan (2003) ArticleTitleA genomewide survey of developmentally relevant genes in Ciona intestinalis.V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway. Dev Genes Evol 213 254–263 Occurrence Handle1:CAS:528:DC%2BD3sXltVWgtrs%3D Occurrence Handle12739141

    CAS  PubMed  Google Scholar 

  71. M Schubert LZ Holland GD Panopoulou H Lehrach ND Holland (2000) ArticleTitleCharacterization of amphioxus AmphiWnt8: Insights into the evolution of patterning of the embryonic dorsoventral axis. Evol Dev 2 85–92 Occurrence Handle10.1046/j.1525-142x.2000.00047.x Occurrence Handle1:CAS:528:DC%2BD38XisVWmsrc%3D Occurrence Handle11258394

    Article  CAS  PubMed  Google Scholar 

  72. K Schughart C Kappen FH Ruddle (1989) ArticleTitleDuplication of large genomic regions during the evolution of vertebrate homeobox genes. Proc Natl Acad Sci USA 86 7067–7071 Occurrence Handle1:CAS:528:DyaL1MXlvVyltLk%3D Occurrence Handle2571149

    CAS  PubMed  Google Scholar 

  73. SM Shimeld PWH Holland (2000) ArticleTitleVertebrate innovations. Proc Natl Acad Sci USA 97 4449–4452 Occurrence Handle10.1073/pnas.97.9.4449 Occurrence Handle1:CAS:528:DC%2BD3cXivFKjs7g%3D Occurrence Handle10781042

    Article  CAS  PubMed  Google Scholar 

  74. A Sidow (1996) ArticleTitleGen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6 715–722 Occurrence Handle1:CAS:528:DyaK2sXhsVWjsw%3D%3D Occurrence Handle8994842

    CAS  PubMed  Google Scholar 

  75. L Skrabanek KH WoIfe (1998) ArticleTitleEukaryote genome duplication—Where’s the evidence? Curr Opin Genet Dev 8 694–700

    Google Scholar 

  76. NG Smith R Knight LD Hurst (1999) ArticleTitleVertebrate genome evolution: A slow shuffle or a big bang? Bioessays 21 697–703 Occurrence Handle1:STN:280:DyaK1MzmvFKgtw%3D%3D Occurrence Handle10440866

    CAS  PubMed  Google Scholar 

  77. J Spring (1997) ArticleTitleVertebrate evolution by interspecific hybridisation—Are we polyploid? FEES Lett 400 2–8 Occurrence Handle10.1016/S0014-5793(96)01351-8 Occurrence Handle1:CAS:528:DyaK28XnsFSmsrg%3D

    Article  CAS  Google Scholar 

  78. T Stach JM Turbeville (2002) ArticleTitlePhylogeny of Tunicata inferred from molecular and morphological characters. Mol Phylogenet Evol 25 408–428 Occurrence Handle10.1016/S1055-7903(02)00305-6 Occurrence Handle1:CAS:528:DC%2BD38Xosl2gurY%3D Occurrence Handle12450747

    Article  CAS  PubMed  Google Scholar 

  79. JS Taylor H Brinkmann (2001) ArticleTitle2R or not 2R? Trends Genet 17 48–489 Occurrence Handle10.1054/ambm.2000.0292

    Article  Google Scholar 

  80. InstitutionalAuthorNameThe Arabidopsis Genome Initiative (2000) ArticleTitleAnalysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 796–815 Occurrence Handle11130711

    PubMed  Google Scholar 

  81. InstitutionalAuthorNameThe Arabidopsis Genome InitiativeThe C. elegans Sequencing Consortium (1998) ArticleTitleGenome sequence of the nematode C. elegans: A platform for investigating biology. Science 282 2012–2018 Occurrence Handle9851916

    PubMed  Google Scholar 

  82. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins (1997) ArticleTitleThe ClustalX windows interface: Flexible strategies or multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24 4876–4882 Occurrence Handle10.1093/nar/25.24.4876

    Article  Google Scholar 

  83. JR True SB Carroll (2002) ArticleTitleGene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 18 53–80 Occurrence Handle10.1146/annurev.cellbio.18.020402.140619 Occurrence Handle1:CAS:528:DC%2BD38XptVOru7g%3D Occurrence Handle12142278

    Article  CAS  PubMed  Google Scholar 

  84. JC Venter et al. (2001) ArticleTitleThe sequence of the human genome. Science 291 1304–1351 Occurrence Handle1:CAS:528:DC%2BD3MXhtlSgsbo%3D Occurrence Handle11181995

    CAS  PubMed  Google Scholar 

  85. A Wagner (2001) ArticleTitleBirth and death of duplicated genes in completely sequenced eukaryotes. Trends Genet 17 237–239 Occurrence Handle1:CAS:528:DC%2BD3MXjtFCltbo%3D Occurrence Handle11335019

    CAS  PubMed  Google Scholar 

  86. Y Wang X Gu (2000) ArticleTitleEvolutionary patterns of gene families generated in the early stage of vertebrates. J Mol Evol 51 88–96 Occurrence Handle1:CAS:528:DC%2BD3cXlslyls7Y%3D Occurrence Handle10903375

    CAS  PubMed  Google Scholar 

  87. KH Wolfe (2001) ArticleTitleYesterday’s polyploids and the mystery of diploidization. Nat Rev Genet 2 333–341 Occurrence Handle10.1038/35072009 Occurrence Handle1:CAS:528:DC%2BD3MXjtlGjs7g%3D Occurrence Handle11331899

    Article  CAS  PubMed  Google Scholar 

  88. KH Wolfe DC Shields (1997) ArticleTitleMolecular evidence for an ancient duplication of the entire yeast genome. Nature 387 708–713 Occurrence Handle1:STN:280:ByiA3snhtVU%3D Occurrence Handle9192896

    CAS  PubMed  Google Scholar 

  89. K Yagi Y Satou F Mazet SM Shimeld B Degnan D Rokhsar M Levine Y Kohara N Satoh (2003) ArticleTitleA genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFkappaB. Dev Genes Evol 213 235–244 Occurrence Handle1:CAS:528:DC%2BD3sXltVWgt7s%3D Occurrence Handle12743820

    CAS  PubMed  Google Scholar 

  90. L Yamada K Kobayashi B Degnan N Satoh Y Satou (2003) ArticleTitleA genomewide survey of developmentally relevant genes in Ciona intestinalis. IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail. Dev Genes Evol 213 245–253 Occurrence Handle1:CAS:528:DC%2BD3sXltVWgt7o%3D Occurrence Handle12743819

    CAS  PubMed  Google Scholar 

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Acknowledgements

This work has been supported by Inserm, Institut Paoli-Calmettes, CNRS, and grants from the Ligue Nationale pour la Recherche centre le Cancer (label). M.L. is the recipient of a fellowship from the Ministère de la Recherche.

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Authors and Affiliations

  1. Département d’Oncologie Moléculaire, Unité 119 INSERM, IFR57, Marseille, France

    Magalie Leveugle, Karine Prat, Cornel Popovici, Daniel Birnbaum & François Coulier

  2. Université de la Méditerranée, Marseille, France

    Magalie Leveugle & François Coulier

  3. Laboratoire de Minéralogie-Cristallographie LMCP, CNRS-UMR 7590C, Paris, France

    Karine Prat

  4. Atelier de Bioinformatique, INSERM Unité 119, Marseille, France

    François Coulier

Authors
  1. Magalie Leveugle
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  2. Karine Prat
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  3. Cornel Popovici
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  4. Daniel Birnbaum
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  5. François Coulier
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Corresponding author

Correspondence to François Coulier.

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Leveugle, M., Prat, K., Popovici, C. et al. Phylogenetic Analysis of Ciona intestinalis Gene Superfamilies Supports the Hypothesis of Successive Gene Expansions . J Mol Evol 58, 168–181 (2004). https://doi.org/10.1007/s00239-003-2538-y

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  • DOI: https://doi.org/10.1007/s00239-003-2538-y

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