Early lineage divergence segregates sensory and non-sensory thalamic circuits

The thalamus integrates sensory, motor, and associative functions via distinct nuclei, yet the developmental principles driving their specification remains unclear. Here, we generate a spatiotemporal single-cell multiomic and spatial transcriptomic atlas of the embryonic mouse thalamus, combined with barcoding-based lineage tracing. We identify two major glutamatergic lineages—sensory and motor/associative—each governed by different gene regulatory programs and temporal dynamics. These lineages arise from spatially and molecularly isolated progenitors, revealing an early segregation of functional identities. Within the sensory lineage, we resolve two discrete trajectories leading to first-order visual and somatosensory neurons, both emerging from a shared higher-order default state. Using in silico predictions and in vivo perturbations, we identify Sp9 as a key regulator of visual thalamic fate. Together, our findings define the molecular architecture and developmental trajectories that underpin thalamic modality specification, providing a framework to understand how functional circuits emerge in the mammalian brain.