Fig. 3: Synapse-related genes are conserved between mouse and tree shrew sSC neurons.

A Heatmap showing the expression of the top 500 genes enriched in tree shrews, mice or shared by the two species. B Enriched Gene Ontology (GO) terms related to biological processes for the top 1600 shared genes. The analysis was performed using a one-sided hypergeometric test with Benjamini-Hochberg correction for multiple comparisons. C Percentage distribution of species specificity index (SSI) for all genes, synapse-related genes, and postsynapse-related genes. Positive x-axis values: higher gene expression in tree shrews; negative: higher in mice. D SynGO enrichment analysis for the top 1600 shared genes in the aspect of cellular components. The analysis was performed using a one-sided Fisher exact test with Bonferroni correction for multiple comparisons. E Violin plot showing Camk2a expression in inhibitory and excitatory neurons by species in the snRNA-seq dataset. Each dot represents an individual neuron. F FISH of Camk2a and Gad1 transcripts in the tree shrew SC. The area in the white square is shown at a higher magnification on the right. Arrows point to example cells co-expressing Camk2a and Gad1. Scale bars: 500 μm (left) and 50 μm (right). G FISH of vGAT and vGluT2 expression in the mouse SC, with neurons labeled by AAV-Camk2a-GFP. Arrows indicate example cells where GFP + neurons co-localized with vGAT, whereas arrowheads indicate the colocalization of GFP and vGluT2 expression. Scale bars: 200 μm (left) and 50 μm (right). H Percentage of Camk2a + cells co-localized with inhibitory markers in mice and tree shrews based on RNA FISH. Mean ± SEM. n = 12 ROIs in tree shrews and 13 ROIs in mice; n = 3 animals each. I Example clusters showing co-expression of cluster markers related to synaptic functions and inhibitory or excitatory markers. J, K FISH of Cbln2 and vGluT2 expression in tree shrews (J) and mice (K). Arrows point to example cells co-expressing Cbln2 and vGluT2. Scale bar, 500 μm (J, left), 200 μm (K, left), and 50 μm (right). L Percentage of Cbln2 + cells co-expressing vGluT2. Mean ± SEM. n = 16 ROIs in tree shrews and 24 ROIs in mice; n = 3 animals each.