Fig. 1

A transcriptomic screen for olfactory subsystem-specific genes. A Top: schematic of the D. melanogaster antennal olfactory subsystems. Bottom: schematic of the comparative antennal transcriptomics experiment of ato mutant (ato¹/Df(3R)p13) and amos mutant (amos³) animals. B Heatmap showing differential expression of chemosensory receptor gene families (odorant receptor (Or), ionotropic receptor (Ir), and gustatory receptor (Gr)) in ato and amos antennal transcriptomes. The enrichment (or non-enrichment) of genes is as expected in all cases (see “Results”), with a few exceptions: (i) Or33c and Or42a are thought to be expressed specifically in the maxillary palp [17, 28]; however, Or33c was previously detected in the antenna by qRT-PCR [16] and Or42a transcripts have been detected in some Orco-negative neurons in the Fly Cell Atlas [29]. Ir68a encodes a hygroreceptor that acts in sacculus neurons [30], although transcripts of this gene appear to be expressed at low levels [31]. C Bar chart comparing the classification of Ir and Or subsystem-enriched genes into the indicated categories (see Additional file 4: Table S1). D Left: t-distributed stochastic neighbor embedding (tSNE) representation of RNA-seq datasets from individual antennal cells from the Fly Cell Atlas (10× stringent dataset in this and all subsequent figures) [29], colored for expression of the neuronal marker N-syb, which is expressed in OSNs, Johnston’s organ auditory neurons, and a neuron population of unknown identity (marked “?”; these also express the mechanoreceptor NompC, suggesting that they are auditory/mechanosensory, rather than olfactory). Right: bar chart of the expression of olfactory subsystem-enriched genes in neuronal and non-neuronal antennal cell populations (see Additional file 4: Table S1). E Top: tSNE plot of antennal single-cell transcriptomes colored for expression of Or and Ir co-receptors, which demarcate the two olfactory subsystems (although Ir25a is expressed at low levels across both subsystems [26, 32]). The Gr21a/Gr63a cell cluster is also indicated; although these do not express Orco, they are considered part of the Or subsystem. Bottom left: tSNE plots colored for expression of the Or subsystem-enriched GstE4 and Ir subsystem-enriched Tsp47F. Bottom right: combined RNA FISH and immunofluorescence for GstE4 and Orco (top) or Tsp47F and Ir8a (bottom) on whole-mount antennae of control (w¹¹¹⁸) animals confirming the broad, subsystem-enriched neuronal expression of these genes. Scale bars, 20 μm