A single-cell transcriptomic atlas of developing inhibitory neurons reveals expanding and contracting modes of diversification

The cerebral cortex relies on vastly different types of inhibitory neurons to compute. How this diversity emerges during development remains an open question. The rarity of individual inhibitory neuron types often leads to their underrepresentation in single-cell RNA sequencing (scRNAseq) datasets, limiting insights into their developmental trajectories. To address this problem, we developed a computational pipeline to enrich and integrate rare cell types across multiple datasets. Applying this approach to somatostatin-expressing (SST+) inhibitory neurons—the most diverse inhibitory cell class in the cortex—we constructed the Dev-SST-Atlas, a comprehensive resource containing mouse transcriptomic data of over 51,000 SST+ neurons. We identify three principal groups—Martinotti cells (MCs), non-Martinotti cells (nMCs), and long-range projecting neurons (LRPs)—each following distinct diversification trajectories. MCs commit early, with distinct embryonic and neonatal clusters that map directly to adult counterparts. In contrast, nMCs diversify gradually, with each developmental cluster giving rise to multiple adult cell types. LRPs follow a unique ‘contracting’ mode. Initially, two clusters are present until postnatal day 5 (P5), but by P7, one type is eliminated through programmed cell death, leaving a single surviving population. This transient LRP type is also found in the fetal human cortex, revealing an evolutionarily conserved feature of cortical development. Together, these findings highlight three distinct modes of SST+ neuron diversification—invariant, expanding, and contracting—offering a new framework to understand how the large repertoire of inhibitory neurons emerges during development.