Physical and functional organization of the AgMNPV-2D genome. The outer and the inner ring represent ORFs in positive and negative sense, respectively. The outer numbering means the AgMNPV-2D ORF numbers (Additional file 1: Table S1), and the inner numbering indicates the loci of the 22 regions of overlapping transcription (ROTs) (for further information, see Additional file 6: Table S3). ROTs with co-occurrence events are shown in bold. ORFs colored in black represent those whose expression profile was not included in the present work (ORFs 64, 83 and 135). A. Genomic map relating the physical position of genes to their distribution among the five regulatory modules (communities) of the GRN. B. Genomic map showing the gene promoter motifs arrangement in the AgMNPV genome. C. Genomic map presenting the genome organization according to gene functions.