Single-cell genomics of the mouse olfactory cortex reveals contrasts with neocortex and ancestral signatures of cell type evolution

Understanding the molecular logic of cortical cell-type diversity can illuminate cortical circuit function and evolution. Here, we performed single-nucleus transcriptome and chromatin accessibility analyses to compare neurons across three- to six-layered cortical areas of adult mice and across tetrapod species. We found that, in contrast to the six-layered neocortex, glutamatergic neurons of the three-layered mouse olfactory (piriform) cortex displayed continuous rather than discrete variation in transcriptomic profiles. Subsets of piriform and neocortical glutamatergic cells with conserved transcriptomic profiles were distinguished by distinct, area-specific epigenetic states. Furthermore, we identified a prominent population of immature neurons in piriform cortex and observed that, in contrast to the neocortex, piriform cortex exhibited divergence between glutamatergic cells in laboratory versus wild-derived mice. Finally, we showed that piriform neurons displayed greater transcriptomic similarity to cortical neurons of turtles, lizards and salamanders than to those of the neocortex. In summary, despite over 200 million years of coevolution alongside the neocortex, olfactory cortex neurons retain molecular signatures of ancestral cortical identity.

Mammalian olfactory cortex neurons retain molecular signatures of ancestral cell types

The cerebral cortex diversified extensively during vertebrate evolution. Intriguingly, the three-layered mammalian olfactory cortex resembles the cortical cytoarchitecture of non-mammals yet evolved alongside the six-layered neocortex, enabling unique comparisons for investigating cortical neuron diversification. We performed single-nucleus multiome sequencing across mouse three- to six-layered cortices and compared neuron types across mice, reptiles and salamander. We identified neurons that are olfactory cortex-specific or conserved across mouse cortical areas. However, transcriptomically similar neurons exhibited area-specific epigenetic states. Additionally, the olfactory cortex showed transcriptomic divergence between lab and wild-derived mice, suggesting enhanced circuit plasticity through adult immature neurons. Finally, olfactory cortex neurons displayed marked transcriptomic similarities to reptile and salamander neurons. Together, these data indicate that the mammalian olfactory cortex retains molecular signatures representative of ancestral cortical traits.