Transcript dynamics was studied throughout sporophyte development of two mosses, Physcomitrella patens and Funaria hygrometrica.

Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, relative contribution of these two processes to radical morphological shifts is still poorly understood. Here we use the model system of two mosses, Funaria hygrometrica and Physcomitrella patens, to investigate the molecular mechanisms underlying divergent sporophyte morphologies. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that sporophyte development mainly relies on genes orthologous (shared) between the two species. We further show that orthologous genes frequently experience temporal gene expression shifts between the two species which is apparently linked to their divergent sporophyte morphologies. While the absolute number of species-specific genes expressed during sporophyte development is small, their contribution to the divergent sporophyte morphologies seems also to be important. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators.