Fig. 2

Comparative analysis of gene expression by the prothoracic glands of Bombyx mori and Drosophila melanogaster. a: Correlation between genes expressed by the Bm PGs on V-6 of the 5th instar and genes expressed in the Dm RGs on the wandering stage as described [31]. For each gene that its orthologue was identified in each of the species, the RPGM (Reads Per Gene Model) derived from Bowtie2 for Bm were plotted against the FPKM (Fragments Per Kilobase of transcript per Million of mapped reads) derived from Cufflinks for Dm [31]. Dashed arrows define the values above which all genes are considered as expressed in either species [31]. The circled area indicates a cluster of highly expressed ribosomal proteins in both species (see Additional file 12: Table S11). b: Venn diagram comparing the Dm RG-specific [4] and the Dm RG-enriched genes [31] with the Bm PG-specific [29, 30] and the Bm-PG expressed genes (this study). The adjacent grid highlights the genes found in at least two of these four datasets. c: Venn diagram comparing the ring gland-specific [4], the Dm RG-enriched [31] genes with the PG-specific [29, 30], the PG expressed genes (this study) and the PTTH-regulated genes [4] of Bm. The adjacent grid highlights the genes found in at least three of these five datasets. d: Venn diagram comparing the PTTH-upregulated genes in Bm PGs [4] with the PG-specific genes [29, 30] (see Additional file 13: Table S12). e: Venn diagram comparing the PTTH-downregulated genes in Bm PGs [4] with the PG-specific genes [29, 30] (see Additional file 13: Table S12). f: Proportional representation of Bm and Dm orthologous genes whose Dm RG-specific silencing resulted in the indicated phenotype as described [32]. Green circles show the number of Dm genes whose RG-specific silencing exhibited the indicated phenotype [32], blue circles show the number of their Bm orthologues that were not highly expressed in PGs and the orange circles show the Bm orthologues that were highly expressed in PGs (see Additional file 3: Table S3, Additional file 15: Table S14 and Additional file 16: Table S15). The sum of blue and orange circles for each group is the number of Bm genes orthologous to the Dm genes shown in the green circles (see Additional file 9: Table S8). Circles are proportional to each other for each phenotype described in [32]