Fig. 3: Spatial organization of S. ambofaciens chromosome and transcriptome in absence of metabolic differentiation.

3C-seq and RNA-seq were performed on S. ambofaciens grown in exponential phase in YEME10 medium (24 h, C6 condition). a The normalized contact map was obtained from asynchronous populations. The x and y axes represent the genomic coordinates of the reference genome. To simplify the analyses, TIRs were removed from the reference genome. The color scale reflects the frequency of the contacts between genome loci, from white (rare contacts) to dark purple (frequent contacts). In b, the frontier index analysis is able to detect, for a given genome 10 kb bin, the change in the contact bias with their neighboring bins. Thus, a boundary is defined as any bin in which there is a change in the right bias of contacts towards the left bias (±2 bins, green and orange peaks, respectively). Red and black circles indicate the position of rDNAs (rrn) and highly expressed genes (HEGs), respectively. In c, the DESeq2 normalized counts measured in cells grown in the same condition were mapped on S. ambofaciens chromosome and binned in 10 kb. d The panel highlights genomic and transcriptional features of interest. The right and left compartments were defined owing to the outer boundaries of the central compartment, which correspond to the first and last rDNA operon position (vertical lines). The ‘synteny break right arm’ corresponds to the beginning of the spiramycin BGC. The replicate of this experiment is presented in Supplementary Fig. 6a.