Plant ‘evo-devo’ goes genomic: from candidate genes to regulatory networks

Plant development gives rise to a staggering complexity of morphological structures with different shapes, colors, and functions. Understanding the evolution of control mechanisms that underlie developmental processes provides insights into causes of morphological diversity and, therefore, is of great interest to biologists. New genomic resources and techniques enable biologists to assess for the first time the evolution of developmental regulatory networks at a global scale. Here, we address the question of how comparative regulatory genomics can be used to reveal the evolutionary dynamics of control networks linked to morphological evolution in plants. Plant development gives rise to a staggering complexity of morphological structures with different shapes, colors, and functions. Understanding the evolution of control mechanisms that underlie developmental processes provides insights into causes of morphological diversity and, therefore, is of great interest to biologists. New genomic resources and techniques enable biologists to assess for the first time the evolution of developmental regulatory networks at a global scale. Here, we address the question of how comparative regulatory genomics can be used to reveal the evolutionary dynamics of control networks linked to morphological evolution in plants. collections of TF binding sites and other noncoding DNA that are sufficient to facilitate transcription in a defined spatial and/or temporal expression domain. chromatin immunoprecipitation followed by sequencing. A technique to determine in vivo DNA-bound regions of a protein at a genome-wide scale. treatment of isolated chromatin with DNAseI. DNAseI cuts accessible DNA and the released fragments are then sequenced. This gives an indication of the chromatin state and, if sequenced deep enough, can reveal protein-binding sites. a change in the timing of expression. a change in the place of expression. a family of TFs, present in all groups of eukaryotes. Named after its founding members MCM1 (Saccharomyces cerevisiae), AGAMOUS (Arabidopsis thaliana), DEFICIENS (Antirrhinum majus), and SRF1 (Homo sapiens). influencing more than one trait due to multiple functions of a gene (e.g., a gene that is involved in the growth of both a leaf and a petal). digital quantification of transcriptomes (mRNA) by next-generation sequencing. procedures for the identification of representative sets of ligands for a protein. In the case of DNA-binding proteins, the protein is mixed with a pool of double-stranded, randomized oligonucleotides. Protein–DNA complexes are recovered and the bound DNA is amplified by PCR and subjected to a new round of selection. DNA fragments are sequenced to reveal the binding specificity of the protein. a family of plant transcription factors. The family is named after Tb1 (Zea mays L.), CYCLOIDEA (Antirrhinum majus), and Pcf1 (Oryza sativus).