Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem

The inflorescence meristem (IM) of flowering plants is a stem cell niche that is the source of aboveground organs such as stems and flowers. Although transcriptional profiling has elucidated some cell types within this tissue, the transcriptional dynamics of differentiation from stem cells into the diverse cell types in these organs remain unknown. We used single-nucleus RNA sequencing to characterize the transcriptional landscape of the IM, linking shoot stem cells to early differentiation cell types. Although our analysis of previously known domains uncovered the role of GH3 gene family members in meristematic activity and phyllotaxis, we also identified unknown transcriptional patterns, including early cortex patterning within developing primordia. Trajectory inference analysis revealed the dynamics of the S-G₂-M cell cycle phases, as well as gene expression programs driving differentiation toward specialized cell types such as early primordia, cortex, cambium, xylem, and phloem. Collectively, our findings advance the understanding of the cell fate transcriptional dynamics shaping shoot organ development.