The transcriptome landscape of floral development for the early‐diverging grass Pharus and insights into spikelet evolution

Spikelets represent a key innovation of grasses (Poaceae) with their arrangements in the inflorescence determining cereal yield. Genetic mechanisms underlying spikelet development were mainly investigated in the core grasses. Representing an early-diverging grass lineage, Pharus bears the first evolved spikelets with primitive traits and unisexual flowers, making it ideal for exploring this issue. Here, we generated a comprehensive transcriptome atlas of inflorescence and spikelet development in Pharus latifolius, supported by an improved genome assembly. Six key developmental stages were identified for transcriptomic analyses, revealing dynamic expression programs primarily associated with meristem fate determination at early stages and organ specification later. Particularly, we identified conserved and lineage-specific transcriptional regulators playing key roles in the Pharus sexual differentiation through retention of paralogs and divergent expression. By bridging the knowledge gap between early-diverging and core grasses, our results shed new insights into the spikelet origin and provided valuable data for functional research on cereal grain production.