biostudies-literatureMay AMedical Research CouncilNIH HHSe3003133https://www.ebi.ac.uk/biostudies/studies/S-EPMC12043239biostudies-literatureUnknown23(4)How tissue shape and therefore function is encoded by the genome remains in many cases unresolved. The tubes of the salivary glands in the Drosophila embryo start from simple epithelial placodes, specified through the homeotic factors Scr/Hth/Exd. Previous work indicated that early morphogenetic changes are prepatterned by transcriptional changes, but an exhaustive transcriptional blueprint driving physical changes was lacking. We performed single-cell-RNAseq-analysis of FACS-isolated early placodal cells, making up less than 0.4% of cells within the embryo. Differential expression analysis in comparison to epidermal cells analyzed in parallel generated a repertoire of genes highly upregulated within placodal cells prior to morphogenetic changes. Furthermore, clustering and pseudotime analPLoS biologySingle-cell analysis of the early Drosophila salivary gland reveals that morphogenetic control involves both the induction and exclusion of gene expression programs.PMC12043239MC_UP_1201/11P40 OD018537Roper KMay AfalseSingle-cell analysis of the early Drosophila salivary gland reveals that morphogenetic control involves both the induction and exclusion of gene expression programs.How tissue shape and therefore function is encoded by the genome remains in many cases unresolved. The tubes of the salivary glands in the Drosophila embryo start from simple epithelial placodes, specified through the homeotic factors Scr/Hth/Exd. Previous work indicated that early morphogenetic changes are prepatterned by transcriptional changes, but an exhaustive transcriptional blueprint driving physical changes was lacking. We performed single-cell-RNAseq-analysis of FACS-isolated early placodal cells, making up less than 0.4% of cells within the embryo. Differential expression analysis in comparison to epidermal cells analyzed in parallel generated a repertoire of genes highly upregulated within placodal cells prior to morphogenetic changes. Furthermore, clustering and pseudotime anal2025-01-01T00:00:00Z2025 Apr2026-06-01T19:13:08.097Z2025-07-06T03:05:52.856ZS-EPMC120432394025807910.1371/journal.pbio.3003133