Fig. 3

The Rhodobacter sphaeroides transcriptome composition is strongly influenced in the PNPase mutant. a Volcano plot of the observed log₂-fold changes based on RNA-Seq data analyzed with DESeq2. Genes with significant change in abundance are colored red (adjusted p-value ≤0.05, log₂fold change ≤ − 1 or ≥ + 1, basemean ≥50) and pink (adjusted p-value ≤0.05, log₂-fold change < − 1 or > + 1, basemean < 50). Grey dots: adjusted p-value > 0.05 or − 1 ≤ log₂-fold change ≥ + 1. Altogether the transcripts of 334 genes were observed to differ in a statistically significant manner and exhibited a basemean above the threshold. b Feature-wise distribution of these significant genes, classified in decreased and increased abundance (pnp mutant/wild type). Most tRNAs and all rRNAs showed a reduced abundance in the mutant strain. x-axis: feature class; y-axis: percentage of differentially expressed genes per feature class [%] c) Comparison of data computed with DESeq2 and baySeq, which show a very good match. Almost all transcripts that are lower abundant in the pnp mutant according to DESeq2 (log₂-fold change (pnp/wt) < 0) are also classified to be lower abundant by baySeq (pnp < wt) and vice versa. Since baySeq does not provide p-values, the color coding represents the square root of the product of the false discovery rate (FDR, obtained from baySeq) and the adjusted p-value (obtained from DESeq2). Every dot represents one gene