Conifers are essential components of forest ecosystems; however, their reproductive development remains largely understudied due to their genomes’ complexity. 

Here, we present a time-resolved spatial transcriptomics (ST) atlas of 88 tissue sections across three time points from developing reproductive and vegetative shoots in wild type Norway spruce (Picea abies) as well as transition shoots from the acrocona mutant. By comparing their different spatiotemporal gene expression dynamics, we identified the molecular processes responsible for the vegetative-to-reproductive shift, which occupy specific spatial domains in the shoots. We also discovered a new gene, DAL55, involved in the reproductive signaling cascade. Moreover, we shed light on the evolutionary relationships between gymnosperm and angiosperm YABBY genes, which are responsible for inner or outer cell layers in complex structures. 

Overall, our spatiotemporal atlas identifies genes, pathways and evolutionary relationships associated with plant reproductive organs; providing a valuable resource for studying conifer reproductive development.