Transgenic tools targeting striatal and pallidal subpopulations reveal both evolutionary conservation and specialization of cortico-basal ganglia circuits in zebrafish

The cortico-basal ganglia circuit mediates decision-making. Here, we generated transgenic tools for adult zebrafish targeting specific subpopulations of the components of this circuit and utilized them to identify evolutionary homologs of the mammalian direct- and indirect-pathway striatal neurons which respectively project to the homologs of the internal and external segment of the globus pallidus (dEN and Vl) as in mammals. Unlike in mammals, the Vl mainly projected to the dEN directly, not by way of the subthalamic nucleus. Further single-cell RNA sequencing analysis revealed two pallidal output pathways: a major shortcut pathway directly connecting the dEN with the pallium and the evolutionarily conserved closed loop by way of the thalamus. Our resources and circuit map provide the common basis for the functional study of the basal ganglia in a small and optically tractable zebrafish brain for the comprehensive mechanistic understanding of the cortico-basal ganglia circuit. Overall design: To identify genetic markers of the npy-negative thalamus-projecting neurons in the dEN, we conducted single-cell RNA sequencing analysis. We dissected the dEN and its surrounding regions from six adult individuals of TgBAC(npy:GAL4VP16);Tg(UAS:GFP). We then dissociated the dissected tissue and used the droplet-based 3'end scRNAseq system Chromium (10x Genomics). We obtained transcriptomic data from 3,381 cells and performed unbiased clustering by Seurat.