Fig. 3

Many genes are developmentally regulated during M. xanthus fruiting body formation. Reads generated from WT M. xanthus were mapped and assigned to genes using BWA to the most recent reference genome annotations, and then the changes in gene expression during the commitment to development were quantified using HTseq and DEseq, comparing earlier with later timepoints in all pairwise combinations. Bar graphs represent numbers of genes with higher expression in the earlier timepoint (yellow) or the later timepoint (blue) for each pairwise comparison, and color intensity represents the observed log2fold change in expression. MA-plots (B) were generated for each pairwise comparison between timepoints using the R code provided with DEseq, including apeglm transformation to reduce variance; red points are those with an adjusted P-value of ≤0.01 and triangles represent genes with a log2 fold change that exeeds the maximum value on the Y-axis