title: The analysis of Gene Regulatory Networks in plant evo-devo.
abstract: We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks (GRNs) in the context of plant evolutionary-developmental (evo-devo) biology. Many of the species that occupy key positions in plant phylogeny are poorly adapted as laboratory models and so we focus here on techniques that can be efficiently applied to both model and non-model species of interest to plant evo-devo. We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post-transcriptional, and epigenetic regulatory mechanisms underlying these patterns, in any plant species with a sequenced genome. We furthermore describe how the technique of Protein Resurrection can be used to confirm inferences on ancestral GRNs and also to provide otherwise-inaccessible points of reference in evolutionary histories by exploiting paralogues generated in gene and whole genome duplication events. Finally, we argue for the better integration of molecular data with information from paleobotanical, paleoecological, and paleogeographical studies to provide the fullest possible picture of the processes that have shaped the evolution of plant development.
authors.affiliation: Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Aurélie C M
authors.initials: AC
authors.lastname: Vialette-Guiraud
authors.affiliation: Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Amélie
authors.initials: A
authors.lastname: Andres-Robin
authors.affiliation: Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Chambrier
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive (UMR 5558 - CNRS/université Lyon 1/université de Lyon), Bâtiment Gregor Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France.
authors.forename: Raquel
authors.initials: R
authors.lastname: Tavares
authors.affiliation: Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France charlie.scutt@ens-lyon.fr.
authors.forename: Charles P
authors.initials: CP
authors.lastname: Scutt
mesh_terms: D005075:Biological Evolution; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology*; D063245:Plant Development / Q000235:genetics*; D010944:Plants / Q000235:genetics
keywords: Ancestral Sequence Reconstruction; Gene Regulatory Network; Protein Resurrection; epigenetic regulation; evo-devo; evolutionary-developmental biology; plant; post-transcriptional regulation; transcriptional regulation.