Fig. 7

Gene expression changes in O. lobularis buds during dissociation and reaggregation. A Principal component analysis (PCA) plot of the 5 different conditions sequenced during dissociation and reaggregation. Dissociation time-points are circled in blue, those of reaggregation in pink. Replicates cluster well except for the samples of the first hour of reaggregation (1hR) which show larger dispersion, and which are located between time-points of four hours of dissociation (4hD) and three hours of reaggregation (3hR), indicating different reaggregation states of the sequenced buds. B A total of 5903 differentially expressed genes (DEGs) were found during dissociation and reaggregation with a log2 fold change (log2|FC|) of at least 1.5 (Additional file 9: Table S6). Pairwise comparisons were done as follows: for dissociation (1hD/CT, 4hD/CT); for reaggregation (1hR/4hD, 3hR/4hD); genes in common for both processes are shown as overlapping (680 genes). Gene ontology enrichment analysis of genes differentially expressed during dissociation shows that genes relevant for the process under study are enriched, including those involved in cell adhesion and its regulation, substrate dependent cell migration and actin bundle assembly were enriched (Additional file 11: Table S8). Enriched GO terms for shared DEGs of both conditions included cell migration, cell adhesion, regulation of collagen metabolic processes as well as integrin-mediated signaling pathway. During reaggregation, relevant GO terms associated with cell adhesion, regulation of integrin and actin filament-based process were enriched. C Phylostratigraphy analyses on the whole transcriptome and during dissociation and reaggregation provide the evolutionary age of differentially regulated genes during the dissociation and reaggregation process, as well as in the entire transcriptome of mixed stages. On the entire transcriptome 16.6% (5389) of the genes are O. lobularis specific (see Additional file 10: Table S7). During dissociation and reaggregation, there is a higher percentage of sponge-specific DEGs as compared to the entire transcriptome. The percentage of metazoan DEGs is higher during dissociation than during reaggregation. Analysis was done after Sogabe and collaborators in[133]. Species used are listed in Additional file 10: Table S7A. D Heatmap showing the hundred most differentially regulated genes during dissociation and reaggregation (1hD/CT, 4hD/CT, 1hR/4hD, 3hR/4hD). For genes upregulated during dissociation or reaggregation, we performed enrichment analysis for GO terms (with TopGO [4]) (Additional file 11: Table S8B). Among the top enriched GO terms, we found regulation of extracellular matrix disassembly for dissociation and establishment and maintenance of an epithelium for the reaggregation