Fig. 5: Defense systems are expressed cyclically.

A Organization of the different defense cassettes in the S. islandicus REY15A genome. CRISPR-Cas and Hma loci of REY15A are shown with different color-coded boxes. A diagonal dotted dash indicates a gap between the genes or cassettes. B Expression of the different defense related genes and cassettes throughout the cell cycle. Pair-wise comparisons between phases are represented in three volcano plots. The y-axis represents the adjusted p value in logarithmic scale in base 10. The x-axis represents the fold change (FC) between the two phases in logarithmic scale in base 2. The horizontal lines mark the threshold for significance, i.e., a p value of <0.01 (-log₁₀(0.01) = 2). The vertical lines mark the threshold for strong differential expression, i.e., FC of 2 (log₂(±2) = ± 1). Statistical significance is extracted from the DGE analysis (Supplementary Data 1), where it was calculated with the limma package and p values were adjusted for multiple comparisons using the Benjamini-Hochberg method. Defense genes and cassettes are highlighted and color-coded. C Gene co-expression subnetworks of the defense components. The subnetworks are extracted from the full GCNs by maintaining only those nodes that co-express with at least two defense-related (CRISPR-Cas or hma) genes. Nodes are colored by arCOG category following the same color code as in Fig. 2B, while edges are colored green if the co-expression is positive and red if it is negative. C inset. Size of the co-expression subnetwork of the CRISPR-Cas interference cassettes and the Hma cassette throughout the cell cycle. Line plot representing the number of nodes of the subnetwork of all genes co-expressing with the Cmr-β, the Cascade, the Cmr-α and the Hma cassettes at each of the phases of the cell cycle.