title: Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.
abstract: We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, "DicotSyntenyViewer" (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.
authors: INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.
authors: Florent
authors: F
authors: Murat
authors: INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.
authors: Rongzhi
authors: R
authors: Zhang
authors: INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France.
authors: Sébastien
authors: S
authors: Guizard
authors: Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
authors: Haris
authors: H
authors: Gavranović
authors: INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.
authors: Raphael
authors: R
authors: Flores
authors: INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.
authors: Delphine
authors: D
authors: Steinbach
authors: INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France.
authors: Hadi
authors: H
authors: Quesneville
authors: INRIA Rhône-Alpes, Université de Lyon 1, CNRS UMR5558, Laboratoire Biométrie et Biologie Évolutive, Villeurbanne Cedex, France.
authors: Eric
authors: E
authors: Tannier
authors: INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France jsalse@clermont.inra.fr.
authors: Jérôme
authors: J
authors: Salse
mesh_terms: D032461:Chromosomes, Plant; D018556:Crops, Agricultural / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D023061:Gene Order; D018745:Genome, Plant; D023281:Genomics; D059785:Karyotype; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011123:Polyploidy; D026801:Synteny
keywords: dominance; evolution; paleogenomics; plasticity; polyploidy
references: Nat Commun. 2012;3:1318
references: 23271652
references: Genome Res. 2013 Feb;23(2):396-408
references: 23149293
references: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19363-8
references: 18048334
references: Genome Res. 2010 Nov;20(11):1545-57
references: 20876790
references: Curr Opin Plant Biol. 2005 Apr;8(2):155-62
references: 15752995
references: Funct Integr Genomics. 2011 Mar;11(1):71-83
references: 20697765
references: Trends Ecol Evol. 1995 Apr;10(4):143-7
references: 21236983
references: Curr Opin Plant Biol. 2012 Apr;15(2):122-30
references: 22280839
references: Nat Genet. 1998 Sep;20(1):43-5
references: 9731528
references: Genome Res. 2007 Sep;17(9):1254-65
references: 17652425
references: BMC Genomics. 2012 Jun 06;13:221
references: 22672222
references: Genome Res. 2006 Jun;16(6):738-49
references: 16702410
references: Curr Opin Plant Biol. 2009 Apr;12(2):119-25
references: 19095493
references: Mol Biol Evol. 2015 Jan;32(1):193-210
references: 25349287
references: Nat Genet. 2011 Feb;43(2):109-16
references: 21186353
references: Nucleic Acids Res. 2003 Feb 15;31(4):1339-50
references: 12582254
references: Nature. 2008 Apr 24;452(7190):991-6
references: 18432245
references: Science. 2009 Nov 20;326(5956):1112-5
references: 19965430
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D1152-8
references: 23180799
references: Nature. 2004 Apr 8;428(6983):617-24
references: 15004568
references: Bioinformatics. 2012 Sep 15;28(18):2388-90
references: 22820205
references: Nature. 2004 Oct 21;431(7011):946-57
references: 15496914
references: Trends Plant Sci. 2006 Jun;11(6):267-73
references: 16690345
references: Nature. 2009 Jan 29;457(7229):551-6
references: 19189423
references: Trends Genet. 2006 Apr;22(4):203-10
references: 16517001
references: PLoS One. 2012;7(5):e36442
references: 22567157
references: Genetics. 2003 Oct;165(2):821-33
references: 14573491
references: Nat Genet. 2011 Feb;43(2):101-8
references: 21186351
references: Nature. 2005 Aug 11;436(7052):793-800
references: 16100779
references: BMC Genomics. 2014 Jun 19;15:498
references: 24948032
references: Plant J. 2013 Jan;73(1):143-53
references: 22974547
references: Brief Bioinform. 2009 Nov;10(6):619-30
references: 19720678
references: Plant J. 2011 Apr;66(1):58-65
references: 21443623
references: Nature. 2010 Jan 14;463(7278):178-83
references: 20075913
references: Science. 2006 Sep 15;313(5793):1596-604
references: 16973872
references: Genome Biol Evol. 2012;4(9):917-28
references: 22833223
references: Nature. 2010 Feb 11;463(7282):763-8
references: 20148030
references: Theor Appl Genet. 2012 Apr;124(6):1059-77
references: 22215248
references: Genetics. 2007 Aug;176(4):2577-88
references: 17565937
references: PLoS One. 2012;7(1):e29762
references: 22253773
references: Bioinformatics. 2011 Jul 1;27(13):i257-65
references: 21685079
references: Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14908-13
references: 19706486
references: Curr Biol. 1995 Jul 1;5(7):737-9
references: 7583118
references: Genome Biol. 2012 Jan 26;13(1):R3
references: 22280555
references: Nat Rev Genet. 2009 Oct;10(10):725-32
references: 19652647
references: Nature. 2000 Dec 14;408(6814):796-815
references: 11130711
references: DNA Res. 2008 Aug;15(4):227-39
references: 18511435
references: Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10274-9
references: 8816790
references: Plant J. 2013 Dec;76(6):1030-44
references: 24164652
references: Genetics. 2005 Apr;169(4):2209-23
references: 15687268
references: Bioinformatics. 2011 Oct 1;27(19):2664-71
references: 21846735
references: Genome Biol Evol. 2012;4(3):265-77
references: 22275519
references: Nat Genet. 2013 May;45(5):487-94
references: 23525075
references: Nat Genet. 2010 Oct;42(10):833-9
references: 20802477
references: Plant J. 2011 Mar;65(5):745-56
references: 21251102
references: Genetics. 2012 Apr;190(4):1563-74
references: 22308264
references: Funct Integr Genomics. 2009 Nov;9(4):473-84
references: 19575250
references: Genome Biol Evol. 2014 Jan;6(1):12-33
references: 24317974
references: Proc Natl Acad Sci U S A. 2009 Apr 7;106(14 ):5737-42
references: 19325131
references: Nature. 2007 Sep 27;449(7161):463-7
references: 17721507