title: Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family.
abstract: BACKGROUND
  GATA transcription factors influence many developmental processes, including the specification of embryonic germ layers. The GATA gene family has significantly expanded in many animal lineages: whereas diverse cnidarians have only one GATA transcription factor, six GATA genes have been identified in many vertebrates, five in many insects, and eleven to thirteen in Caenorhabditis nematodes. All bilaterian animal genomes have at least one member each of two classes, GATA123 and GATA456.
  
  
  RESULTS
  We have identified one GATA123 gene and one GATA456 gene from the genomic sequence of two invertebrate deuterostomes, a cephalochordate (Branchiostoma floridae) and a hemichordate (Saccoglossus kowalevskii). We also have confirmed the presence of six GATA genes in all vertebrate genomes, as well as additional GATA genes in teleost fish. Analyses of conserved sequence motifs and of changes to the exon-intron structure, and molecular phylogenetic analyses of these deuterostome GATA genes support their origin from two ancestral deuterostome genes, one GATA 123 and one GATA456. Comparison of the conserved genomic organization across vertebrates identified eighteen paralogous gene families linked to multiple vertebrate GATA genes (GATA paralogons), providing the strongest evidence yet for expansion of vertebrate GATA gene families via genome duplication events.
  
  
  CONCLUSIONS
  From our analysis, we infer the evolutionary birth order and relationships among vertebrate GATA transcription factors, and define their expansion via multiple rounds of whole genome duplication events. As the genomes of four independent invertebrate deuterostome lineages contain single copy GATA123 and GATA456 genes, we infer that the 0R (pre-genome duplication) invertebrate deuterostome ancestor also had two GATA genes, one of each class. Synteny analyses identify duplications of paralogous chromosomal regions (paralogons), from single ancestral vertebrate GATA123 and GATA456 chromosomes to four paralogons after the first round of vertebrate genome duplication, to seven paralogons after the second round of vertebrate genome duplication, and to fourteen paralogons after the fish-specific 3R genome duplication. The evolutionary analysis of GATA gene origins and relationships may inform understanding vertebrate GATA factor redundancies and specializations.
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA. wgillis@uoregon.edu
authors.forename: William Q
authors.initials: WQ
authors.lastname: Gillis
authors.forename: John
authors.initials: J
authors.lastname: St John
authors.forename: Bruce
authors.initials: B
authors.lastname: Bowerman
authors.forename: Stephan Q
authors.initials: SQ
authors.lastname: Schneider
mesh_terms: D000818:Animals; D002816:Chordata, Nonvertebrate / Q000235:genetics; D055028:Comparative Genomic Hybridization; D017124:Conserved Sequence; D019143:Evolution, Molecular; D050980:GATA Transcription Factors / Q000235:genetics*; D020440:Gene Duplication; D016678:Genome; D007448:Invertebrates / Q000235:genetics; D005810:Multigene Family; D010802:Phylogeny; D022821:RNA Splice Sites; D017422:Sequence Analysis, DNA; D026801:Synteny; D014714:Vertebrates / Q000235:genetics*
chemical_list: D050980:GATA Transcription Factors; D022821:RNA Splice Sites
references.citation: J Exp Zool B Mol Dev Evol. 2007 Sep 15;308(5):563-77
references.pmid: 17068775
references.citation: WormBook. 2005 Jun 25;:1-6
references.pmid: 18023122
references.citation: Biol Direct. 2008 May 21;3:20
references.pmid: 18495041
references.citation: BMC Evol Biol. 2008 Apr 15;8:112
references.pmid: 18412965
references.citation: Mol Phylogenet Evol. 2002 Sep;24(3):358-65
references.pmid: 12220977
references.citation: Curr Opin Genet Dev. 2002 Aug;12(4):416-22
references.pmid: 12100886
references.citation: Dev Biol. 2007 Nov 15;311(2):623-35
references.pmid: 17869240
references.citation: Evol Dev. 2007 Jan-Feb;9(1):39-50
references.pmid: 17227365
references.citation: Philos Trans R Soc Lond B Biol Sci. 2008 Apr 27;363(1496):1569-78
references.pmid: 18192177
references.citation: J Biosci. 2007 Dec;32(7):1273-80
references.pmid: 18202451
references.citation: FEMS Microbiol Lett. 1999 May 15;174(2):247-50
references.pmid: 10339815
references.citation: J Anat. 2001 Jul-Aug;199(Pt 1-2):85-98
references.pmid: 11523831
references.citation: Nature. 2007 Mar 29;446(7135):507-12
references.pmid: 17392779
references.citation: Mol Biol Evol. 2009 Jan;26(1):47-59
references.pmid: 18842688
references.citation: Science. 1998 Nov 27;282(5394):1711-4
references.pmid: 9831563
references.citation: PLoS Biol. 2005 Oct;3(10):e314
references.pmid: 16128622
references.citation: Dev Genes Evol. 1998 Dec;208(10):569-77
references.pmid: 9811975
references.citation: Bioinformatics. 2001 Aug;17(8):754-5
references.pmid: 11524383
references.citation: Nat Genet. 1998 Apr;18(4):345-9
references.pmid: 9537416
references.citation: Bioessays. 2001 Feb;23(2):142-51
references.pmid: 11169587
references.citation: Nature. 2008 Jun 19;453(7198):1064-71
references.pmid: 18563158
references.citation: Dev Dyn. 2005 May;233(1):1-19
references.pmid: 15765512
references.citation: Genetics. 1999 Apr;151(4):1531-45
references.pmid: 10101175
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15386-91
references.pmid: 15494441
references.citation: Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4076-81
references.pmid: 10760276
references.citation: Mol Biol Evol. 2002 Sep;19(9):1440-50
references.pmid: 12200472
references.citation: Hereditas. 1968;59(1):169-87
references.pmid: 5662632
references.citation: Syst Biol. 2003 Oct;52(5):696-704
references.pmid: 14530136
references.citation: Mar Biotechnol (NY). 2008 May-Jun;10(3):227-33
references.pmid: 18297360
references.citation: Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4469-74
references.pmid: 10781046
references.citation: J Mol Evol. 2000 Feb;50(2):103-15
references.pmid: 10684344
references.citation: Philos Trans R Soc Lond B Biol Sci. 2008 Apr 27;363(1496):1435-43
references.pmid: 18192191
references.citation: Mol Biol Evol. 2005 May;22(5):1246-53
references.pmid: 15703236
references.citation: Genome Res. 1999 Sep;9(9):868-77
references.pmid: 10508846
references.citation: Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6536-41
references.pmid: 15084738
references.citation: Mol Biol Evol. 2005 Nov;22(11):2275-84
references.pmid: 16049193
references.citation: Nat Rev Genet. 2001 May;2(5):333-41
references.pmid: 11331899
references.citation: Dev Biol. 1999 Jun 15;210(2):305-21
references.pmid: 10357893
references.citation: J Mol Evol. 2006 Jun;62(6):772-84
references.pmid: 16752215
references.citation: Semin Cell Dev Biol. 2005 Feb;16(1):83-94
references.pmid: 15659343
references.citation: Mol Biol Evol. 2009 Feb;26(2):463-71
references.pmid: 19029191
references.citation: Syst Biol. 2006 Aug;55(4):539-52
references.pmid: 16785212
references.citation: Development. 2005 Feb;132(4):763-74
references.pmid: 15659482
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Proc Natl Acad Sci U S A. 1998 Jan 20;95(2):606-11
references.pmid: 9435239
references.citation: Methods Mol Biol. 2008;452:365-83
references.pmid: 18566773