title: Evidence for active maintenance of phylotranscriptomic hourglass patterns in animal and plant embryogenesis.
abstract: The developmental hourglass model has been used to describe the morphological transitions of related species throughout embryogenesis. Recently, quantifiable approaches combining transcriptomic and evolutionary information provided novel evidence for the presence of a phylotranscriptomic hourglass pattern across kingdoms. As its biological function is unknown it remains speculative whether this pattern is functional or merely represents a nonfunctional evolutionary relic. The latter would seriously hamper future experimental approaches designed to test hypotheses regarding its function. Here, we address this question by generating transcriptome divergence index (TDI) profiles across embryogenesis of Danio rerio, Drosophila melanogaster, and Arabidopsis thaliana. To enable meaningful evaluation of the resulting patterns, we develop a statistical test that specifically assesses potential hourglass patterns. Based on this objective measure we find that two of these profiles follow a statistically significant hourglass pattern with the most conserved transcriptomes in the phylotypic periods. As the TDI considers only recent evolutionary signals, this indicates that the phylotranscriptomic hourglass pattern is not a rudiment but possibly actively maintained, implicating the existence of some linked biological function associated with embryogenesis in extant species.
authors: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
authors: Hajk-Georg
authors: HG
authors: Drost
authors: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
authors: Alexander
authors: A
authors: Gabel
authors: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany ivo.grosse@informatik.uni-halle.de mquint@ipb-halle.de.
authors: Ivo
authors: I
authors: Grosse
authors: Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany ivo.grosse@informatik.uni-halle.de mquint@ipb-halle.de.
authors: Marcel
authors: M
authors: Quint
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D004331:Drosophila melanogaster / Q000235:genetics* / Q000254:growth & development; D047108:Embryonic Development / Q000235:genetics; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D008957:Models, Genetic; D010802:Phylogeny; D063245:Plant Development / Q000235:genetics; D059467:Transcriptome / Q000235:genetics; D015027:Zebrafish / Q000235:genetics* / Q000254:growth & development
keywords: developmental hourglass; embryogenesis; evo-devo; phylotranscriptomics
references: Nature. 2010 Dec 9;468(7325):815-8
references: 21150997
references: Evol Dev. 2010 Mar-Apr;12(2):144-56
references: 20433455
references: Nature. 2014 Aug 28;512(7515):445-8
references: 25164755
references: Dev Cell. 2012 May 15;22(5):1101-8
references: 22560298
references: Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):E4858-66
references: 24277850
references: Trends Genet. 2007 Nov;23(11):533-9
references: 18029048
references: Evol Dev. 2008 Sep-Oct;10(5):583-90
references: 18803776
references: Bioinformatics. 2006 Dec 1;22(23):2971-2
references: 17021158
references: Trends Ecol Evol. 2012 Jul;27(7):385-93
references: 22520868
references: Nature. 2010 Dec 9;468(7325):811-4
references: 21150996
references: BMC Biol. 2007 Jan 12;5:1
references: 17222327
references: Trends Ecol Evol. 1997 Dec;12(12):461-3
references: 21238158
references: Dev Suppl. 1994;:135-42
references: 7579514
references: J Exp Zool. 2001 Aug 15;291(2):195-204
references: 11479918
references: PLoS One. 2013 Jun 14;8(6):e66826
references: 23799133
references: PLoS Genet. 2008 Dec;4(12):e1000311
references: 19096706
references: Dev Biol. 2010 Jan 1;337(1):157-61
references: 19799894
references: PLoS Genet. 2013 Apr;9(4):e1003476
references: 23637639
references: Nat Genet. 2011 May;43(5):476-81
references: 21478890
references: PLoS One. 2006 Dec 20;1:e85
references: 17183716
references: Nat Genet. 2013 Jun;45(6):701-706
references: 23624526
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
references: 16845082
references: Trends Plant Sci. 2008 Sep;13(9):483-91
references: 18684657
references: Nucleic Acids Res. 2014 Jan;42(Database issue):D749-55
references: 24316576
references: Nucleic Acids Res. 2014 Jan;42(Database issue):D780-8
references: 24234449
references: Nat Commun. 2011;2:248
references: 21427719
references: Science. 2002 Sep 27;297(5590):2270-5
references: 12351791
references: J Mol Evol. 1995 Dec;41(6):1152-9
references: 8587111
references: Plant Cell. 1997 Nov;9(11):1903-1919
references: 12237352
references: Genome Biol Evol. 2014 Aug 27;6(9):2459-67
references: 25169982
references: Bioinformatics. 2003 Nov 22;19(17):2325-7
references: 14630667
references: Proc Biol Sci. 2003 Feb 22;270(1513):341-6
references: 12639312
references: Nature. 2011 Mar 24;471(7339):473-9
references: 21179090
references: Bioessays. 1999 Jul;21(7):604-13
references: 10472187
references: Anat Embryol (Berl). 1997 Aug;196(2):91-106
references: 9278154
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86
references: 22110026
references: Plant Physiol. 2011 May;156(1):346-56
references: 21402797
references: J Mol Evol. 2005 Jun;60(6):774-85
references: 15909223
references: J Exp Zool B Mol Dev Evol. 2005 Mar 15;304(2):150-8
references: 15779077
references: Am J Bot. 2005 Apr;92(4):761-7
references: 21652456
references: Cell. 2011 Mar 18;144(6):970-85
references: 21414487
references: Nature. 2012 Oct 4;490(7418):98-101
references: 22951968
references: Cold Spring Harb Symp Quant Biol. 2009;74:65-80
references: 20375317
references: Dev Biol. 1995 Dec;172(2):412-21
references: 8612960
references: Science. 2002 Feb 22;295(5559):1482-5
references: 11859185