Figure 7. The anterior midgut gut of L. plantarum (Lp)-associated larvae display transcriptomic signatures of remodelling and metabolic switch.
(A) Experimental design of the RNAseq strategy. We looked for genes differentially expressed (DE, red, orange, and yellow lines) or not differentially expressed (not DE, grey line) between conditions. Arrowheads indicate the control condition in each comparison. (B, C) Venn diagram showing the number of genes from each filter. We further selected genes from filter 1 with a Log2 fold change (LogFC) of less than –0.5 for genes down-regulated (B) and more than 0.5 for genes up-regulated (C) for functional enrichment analyses. (D, E) Dot plot of Gene Ontology (GO) enrichment analysis of genes down-regulated (D) or up-regulated (E) by Lp association in a general control nonderepressible 2 (GCN2)-dependent, ATF4-independent, and ribosomal and transfer RNA (r/tRNA) operon-dependent manner. The size of the dots represents the number of DE genes in each category, x-axis represents the gene ratio enrichment in comparison to the complete gene set of D. melanogaster; colour indicates the significance in terms of BH-adjusted p-values. (F,G) Corresponding LogFC plot from filter 1 (control Lp vs control germ-free [GF]) of genes belonging to the GO terms categories in (D) and (E), respectively.
Figure 7—figure supplement 1. 3D principal component analysis (PCA) plot showing the first three components, calculated with a variance stabilising transformation of normalised counts from DESeq2.
