Early lineage divergence segregates sensory and motor-associative identities in the thalamus

The thalamus integrates sensory, motor and associative functions through distinct nuclei, yet the developmental principles driving their specification remain 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-related and motor-associative, each governed by different gene regulatory programs and temporal dynamics. These lineages arise from spatially and molecularly distinct progenitor domains, revealing an early segregation of functional identities. Within the sensory lineage, we resolve branching sensory trajectories leading to first-order visual and somatosensory neurons, both emerging from a shared higher-order-like state. Using in silico predictions and in vivo perturbation, 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. Sensory and motor-associative identities in the thalamus arise from two early-diverging lineages, with sensory neurons progressing through shared intermediate states, revealing how thalamic organization emerges during development.