show Abstracthide AbstractThe extensive diversity for floral branching systems is an excellent example of morphological evolution in plants. This study seeks to advance our understanding of the relationship between floral system complexity and the developmental progression or maturation of plant stem cells, meristems. This was accomplished through transcriptome profiling of sequential meristem developmental stages in five nightshade species representing a continuum of floral branching architectures. Through comparative transcriptome analyses, we demonstrate that altering the rate of meristem developmental progression explains the range of floral system phenotypes. We further show that heterochronic shifts in expression of a relatively small number of genes, many of which are transcription factors, are responsible for modulating meristem maturation schedules, and that the mid-development transition is a critical window for these changes. This study demonstrates that evolutionary diversity for floral branching systems is determined by subtle modifications of transcriptional programs during a critical window of meristem maturation.