Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach

The discovery of Lacandonia (Triuridaceae) in Brazil

(2015) ALINE MELO et al.   Phytotaxa

The role of WOX genes in flower development

(2014) Enrico Costanzo et al.   ANNALS OF BOTANY

Repeated Evolutionary Changes of Leaf Morphology Caused by Mutations to a Homeobox Gene

(2014) Adrien Sicard et al.   CURRENT BIOLOGY

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

(2014) J. Sequeira-Mendes et al.   PLANT CELL

The NTT transcription factor promotes replum development in Arabidopsis fruits

(2014) Nayelli Marsch-Martínez et al.   PLANT JOURNAL

Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene

(2014) D. Vlad et al.   SCIENCE

Origins and Evolution of WUSCHEL-Related Homeobox Protein Family in Plant Kingdom

(2014) Gaibin Lian et al.   TheScientificWorldJOURNAL

Co-option of the polarity gene network shapes filament morphology in angiosperms

(2014) Ana Maria Rocha de Almeida et al.   Scientific Reports

Looking at plant cell cycle from the chromatin window

(2014) Bénédicte Desvoyes et al.   Frontiers in Plant Science

Genomics and the Evolution of Phenotypic Traits

(2013) Gregory A. Wray   Annual Review of Ecology Evolution and Systematics

NATURAL VARIATION IN EPIGENETIC GENE REGULATION AND ITS EFFECTS ON PLANT DEVELOPMENTAL TRAITS

(2013) Franziska Turck et al.   EVOLUTION

Adaxial-abaxial polarity: The developmental basis of leaf shape diversity

(2013) Kenji Fukushima et al.   GENESIS

Genetic Dissection of a Major Anthocyanin QTL Contributing to Pollinator-Mediated Reproductive Isolation Between Sister Species ofMimulus

(2013) Yao-Wu Yuan et al.   GENETICS

The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression

(2013) C. D. Meiklejohn et al.   GENOME RESEARCH

Molecular Evolution Constraints in the Floral Organ Specification Gene Regulatory Network Module across 18 Angiosperm Genomes

(2013) Jose Davila-Velderrain et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reinforcement in plants

(2013) Robin Hopkins   NEW PHYTOLOGIST

Epigenetic regulation of adaptive responses of forest tree species to the environment

(2013) Katharina Bräutigam et al.   Ecology and Evolution

Cell Patterns Emerge from Coupled Chemical and Physical Fields with Cell Proliferation Dynamics: The Arabidopsis thaliana Root as a Study System

(2013) Rafael A. Barrio et al.   PLoS Computational Biology

Finding Missing Interactions of the Arabidopsis thaliana Root Stem Cell Niche Gene Regulatory Network

(2013) Eugenio Azpeitia et al.   Frontiers in Plant Science

Flower color as a model system for studies of plant evo-devo

(2013) James M. Sobel et al.   Frontiers in Plant Science

Dynamic models of epidermal patterning as an approach to plant eco-evo-devo

(2012) Mariana Benítez et al.   CURRENT OPINION IN PLANT BIOLOGY

Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies

(2012) C. Smaczniak et al.   DEVELOPMENT

Gene Duplication and the Evolution of Plant MADS-box Transcription Factors

(2012) Chiara A. Airoldi et al.   Journal of Genetics and Genomics

Leaf adaxial-abaxial polarity specification and lamina outgrowth: evolution and development

(2012) T. Yamaguchi et al.   PLANT AND CELL PHYSIOLOGY

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Reciprocal Loss of CArG-Boxes and Auxin Response Elements Drives Expression Divergence of MPF2-Like MADS-Box Genes Controlling Calyx Inflation

(2012) Muhammad Ramzan Khan et al.   PLoS One

Evolutionarily conserved repressive activity of WOX proteins mediates leaf blade outgrowth and floral organ development in plants

(2012) H. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pollinator-Mediated Selection on Flower Color Allele Drives Reinforcement

(2012) R. Hopkins et al.   SCIENCE

Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects, and Dominance

(2012) Jonathan D. Gruber et al.   PLoS Genetics

A double-flowered variety of lesser periwinkle (Vinca minor fl. pl.) that has persisted in the wild for more than 160 years

(2011) Yong-Qiang Wang et al.   ANNALS OF BOTANY

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Pollinator Choice in Petunia Depends on Two Major Genetic Loci for Floral Scent Production

(2011) Ulrich Klahre et al.   CURRENT BIOLOGY

The Same Regulatory Point Mutation Changed Seed-Dispersal Structures in Evolution and Domestication

(2011) Nicolas Arnaud et al.   CURRENT BIOLOGY

Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events

(2011) D. K. Goode et al.   DEVELOPMENT

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii

(2011) Robin Hopkins et al.   NATURE

INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1

(2011) Luke Ramsay et al.   NATURE GENETICS

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Speciation genes in plants

(2010) Loren H. Rieseberg et al.   ANNALS OF BOTANY

Regulation of plant gene expression by alternative splicing

(2010) Craig G. Simpson et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Arabidopsis thaliana Leaf Form Evolved via Loss of KNOX Expression in Leaves in Association with a Selective Sweep

(2010) Paolo Piazza et al.   CURRENT BIOLOGY

Methylation and demethylation of the Arabidopsis genome

(2010) Ian J Furner et al.   CURRENT OPINION IN PLANT BIOLOGY

KNOX genes: versatile regulators of plant development and diversity

(2010) A. Hay et al.   DEVELOPMENT

Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana

(2010) Oliver Bossdorf et al.   EVOLUTIONARY ECOLOGY

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng et al.   NATURE

Regulation of transcription in plants: mechanisms controlling developmental switches

(2010) Kerstin Kaufmann et al.   NATURE REVIEWS GENETICS

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis

(2010) Carlos M. Herrera et al.   NEW PHYTOLOGIST

The genetic basis of evolutionary change in gene expression levels

(2010) J. J. Emerson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy

(2010) S. F. Gilbert et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Hidden Variability of Floral Homeotic B Genes in Solanaceae Provides a Molecular Basis for the Evolution of Novel Functions

(2010) K. Geuten et al.   PLANT CELL

B-Function Expression in the Flower Center Underlies the Homeotic Phenotype of Lacandonia schismatica (Triuridaceae)

(2010) E. R. Alvarez-Buylla et al.   PLANT CELL

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

(2010) Catarina Fonseca Lira-Medeiros et al.   PLoS One

Flower Development as an Interplay between Dynamical Physical Fields and Genetic Networks

(2010) Rafael Ángel Barrio et al.   PLoS One

Single amino acid change alters the ability to specify male or female organ identity

(2010) C. A. Airoldi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

LEAFY blossoms

(2010) Edwige Moyroud et al.   TRENDS IN PLANT SCIENCE

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

A hitchhiker's guide to the MADS world of plants

(2010) Lydia Gramzow et al.   GENOME BIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes

(2009) Mariana Mondragón-Palomino et al.   ANNALS OF BOTANY

Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

(2009) Mariana Mondragón-Palomino et al.   BMC EVOLUTIONARY BIOLOGY

A Single Amino Acid Replacement in ETC2 Shapes Trichome Patterning in Natural Arabidopsis Populations

(2009) Julia Hilscher et al.   CURRENT BIOLOGY

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium)

(2009) B. Chaudhary et al.   GENETICS

Evolution of petal identity

(2009) V. F. Irish   JOURNAL OF EXPERIMENTAL BOTANY

MPF2-Like-A MADS-Box Genes Control the Inflated Calyx Syndrome in Withania (Solanaceae): Roles of Darwinian Selection

(2009) M. R. Khan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

Genetic changes contributing to the parallel evolution of red floral pigmentation amongIpomoeaspecies

(2009) Matthew A. Streisfeld et al.   NEW PHYTOLOGIST

Multiple Repeats of a Promoter Segment Causes Transcription Factor Autoregulation in Red Apples

(2009) R. V. Espley et al.   PLANT CELL

Stage-Specific Regulation of Solanum lycopersicum Leaf Maturation by Class 1 KNOTTED1-LIKE HOMEOBOX Proteins

(2009) E. Shani et al.   PLANT CELL

The analysis of entire gene promoters by surface plasmon resonance

(2009) Edwige Moyroud et al.   PLANT JOURNAL

From ABC genes to regulatory networks, epigenetic landscapes and flower morphogenesis: Making biological sense of theoretical approaches

(2009) Elena R. Alvarez-Buylla et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower

(2009) Kerstin Kaufmann et al.   PLOS BIOLOGY

The Regulation and Evolution of a Genetic Switch Controlling Sexually Dimorphic Traits in Drosophila

(2008) Thomas M. Williams et al.   CELL

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Population epigenetics

(2008) Eric J Richards   CURRENT OPINION IN GENETICS & DEVELOPMENT

An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development

(2008) E. Chae et al.   DEVELOPMENT

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Epigenetic Modification of Centromeric Chromatin: Hypomethylation of DNA Sequences in the CENH3-Associated Chromatin in Arabidopsis thaliana and Maize

(2008) W. Zhang et al.   PLANT CELL

Overexpression of the maize Teosinte Branched1 gene in wheat suppresses tiller development

(2008) Janet M. Lewis et al.   PLANT CELL REPORTS

Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape

(2008) Elena R. Álvarez-Buylla et al.   PLoS One

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

The gene regulatory logic of transcription factor evolution

(2008) Günter P. Wagner et al.   TRENDS IN ECOLOGY & EVOLUTION

The Evolution of Combinatorial Gene Regulation in Fungi

(2008) Brian B Tuch et al.   PLOS BIOLOGY