A repeated molecular architecture across thalamic pathways

Thalamus is the central communication hub of the forebrain, providing cerebral cortex with inputs from sensory organs, subcortical systems, and cortex itself. Multiple thalamic regions send convergent information to each cortical region, but the organizational logic of thalamic projections has remained elusive. Through comprehensive transcriptional analyses of retrogradely labeled thalamic neurons in adult mice, we identify three major profiles of thalamic pathway. These profiles exist along a continuum that is repeated across all major projection systems, such as those for vision, motor control, and cognition. The largest component of gene expression variation in mouse thalamus is topographically organized with features conserved in humans. Transcriptional differences between these thalamic neuronal identities are tied to cellular features critical for function, such as axonal morphology and membrane properties. Molecular profiling therefore reveals covariation in properties of thalamic pathways serving all major input modalities and output targets, establishing a molecular framework for understanding thalamus.