Additional file 5 of Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain

Additional file 5: Figure S4. Additional single-cell analyses using HSAL50 and HSAL51 annotations. (A) Heatmaps of markers for neurons (nSyb), glia (bdl), mushroom body neurons (mub), and ensheathing glia (Tsf1) in HSAL51 single-cell clustering. (B) Number of marker genes (padj < 0.05, LFC > 1) for each cluster. Marker genes common to HSAL50 and HSAL51 analyses are shown in black, while markers unique to HSAL50 are in gray and markers unique to HSAL51 are in blue. (C) Scatter plot for UMI counts in HSAL50 vs. HSAL51 with marker genes highlighted according to (B). (D) Heatmap of newly identified mushroom body markers in HSAL51 (padj < 0.05 and logFC > 1.5). Arrows denote mushroom body clusters, as determined by mub expression (top row of heatmap). Classification of each new marker in other data sets (fly MB vs head, [43]; fly single-cell, [44]; honeybee single-cell, [45]) is indicated in heatmap to right, with black boxes indicating marker was identified as mushroom body-enriched (see methods). (E) Genome browser view showing CG9259 with RNA-seq, Iso-Seq, and single-cell coverage along with dT-seq and raw Iso-Seq reads. Scales represents counts per million. A subset of HSAL51 isoforms is shown. (F) Number of genes differentially expressed (DE) within each cluster (padj < 0.01). Differentially expressed genes common to HSAL50 and HSAL51 analyses are shown in black, while genes unique to HSAL50 are in gray and genes unique to HSAL51 are in blue. (G) Scatter plot for UMI counts in HSAL50 vs. HSAL51 with differentially expressed genes highlighted according to (F). (H) TPM of CycG in worker (n = 11) and gamergate (n = 12) brains. Padj is from DESeq2.