title: Auxin-induced expression divergence between Arabidopsis species may originate within the TIR1/AFB-AUX/IAA-ARF module.
abstract: Auxin is an essential regulator of plant growth and development, and auxin signaling components are conserved among land plants. Yet, a remarkable degree of natural variation in physiological and transcriptional auxin responses has been described among Arabidopsis thaliana accessions. As intraspecies comparisons offer only limited genetic variation, we here inspect the variation of auxin responses between A. thaliana and A. lyrata. This approach allowed the identification of conserved auxin response genes including novel genes with potential relevance for auxin biology. Furthermore, promoter divergences were analyzed for putative sources of variation. De novo motif discovery identified novel and variants of known elements with potential relevance for auxin responses, emphasizing the complex, and yet elusive, code of element combinations accounting for the diversity in transcriptional auxin responses. Furthermore, network analysis revealed correlations of interspecies differences in the expression of AUX/IAA gene clusters and classic auxin-related genes. We conclude that variation in general transcriptional and physiological auxin responses may originate substantially from functional or transcriptional variations in the TIR1/AFB, AUX/IAA, and ARF signaling network. In that respect, AUX/IAA gene expression divergence potentially reflects differences in the manner in which different species transduce identical auxin signals into gene expression responses.
authors.affiliation: Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann, Halle (Saale), Germany.|Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Trenner
authors.affiliation: German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany.|Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1,Halle (Saale), Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Poeschl
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1,Halle (Saale), Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Grau
authors.affiliation: German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany.|Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1,Halle (Saale), Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gogol-Döring
authors.affiliation: Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann, Halle (Saale), Germany.|Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Quint
authors.affiliation: Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann, Halle (Saale), Germany.|Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), Germany.
authors.forename: Carolin
authors.initials: C
authors.lastname: Delker
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D007210:Indoleacetic Acids / Q000378:metabolism*; D010937:Plant Growth Regulators / Q000378:metabolism*; D015398:Signal Transduction
chemical_list: D029681:Arabidopsis Proteins; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators
keywords: Arabidopsis; auxin; auxin code; comparative transcriptomics; natural variation; profile interaction finder; promoter motif