The spatiotemporal transcriptome dataset reported here provides the peach flower bud’s gene expression atlas at spatiotemporal resolution level using the 10x Genomics Visium platform. This dataset can be used to define transcript accumulation for any interesting genes across several flower bud cells. It was generated using three peach flower bud samples during the activity–dormancy period, providing valuable insight into gene expression profiling and developmental stages under different environmental contexts or conditions. Importantly, we found that different cell types are related to specific regulatory programs, including signal transduction, environment and stress responses, and flower development. Our research provides insight into the transcriptomic landscape of the key cell types for flower buds and opens new avenues to study cell-type specification, function, and differentiation in Rosaceae fruit trees. A series of pivotal genes (e.g. AMS, MS188, MS1) for flower bud development were identified. These results provide a valuable reference for the activity–dormancy transition in perennial deciduous fruit trees.

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