Fig. 6

Gene regulatory network-predicted extent and limitation of known candidate regulators. a Expression (Z-score) of previously known candidate nuclear positive transcriptional regulators of plastid or chloroplast development. The region of transition between the plastid and chloroplast growth phases is shown as a gray band. The individual genes are listed in Additional file 5: Table S4. b Expression of all DYGs for chloroplast-targeted proteins (see “Methods”), displayed according to WGCNA modules as identified in Fig. 2c. Terms on the right show typical overrepresented gene ontology terms for the function of genes in the module. Bars at the bottom refer to the organelle development processes established in Figs. 4 and 5. c GENIE3-generated gene regulatory network providing best-estimate links (or their absence) between previously known chloroplast-related positive transcriptional regulators (a) and DYGs encoding chloroplast proteins (b); the color scale indicates regulatory ranking, gray indicating absolute lack of predicted regulatory association. The separate columns represent the independently computed values for the different homeologs (in most cases three) of each candidate regulator