Figure 3

Genome configurations of A. orientalis and A. mediterranei . (A) All of the dots in the panels were calculated in a 90-kb sliding window. For the broken X plot (lower right of the panel), the dots represent a reciprocal best match between the genomes of A. orientalis and A. mediterranei, based on the BLASTP comparison. The X-axis (Y-axis) is the nucleotide scale of the A. orientalis (A. mediterranei) chromosome. R1 (4.02-4.28 Mb, AORI_3663-AORI_3909) and R2 (5.55-5.75 Mbp, AORI_4997-AORI_5173) were designated as the two quasi-core regions in the A. orientalis genome. Reciprocally, two regions (AMED_4864-AMED_5049 and AMED_5970-AMED_7071) were defined as the quasi-core in the A. mediterranei genome. The core and quasi-core regions are highlighted in lavender (A. orientalis) or in pink (A. mediterranei). P1 to P4 were designated as the regions containing biosynthesis clusters of rifamycin (rif in A. mediterranei), vancomycin (vcm in A. orientalis), NRPS (nrps10 in A. mediterranei) and polyketide (pks9 in A. orientalis), respectively. In the upper right and lower left panels, the pink triangles represent the coding density of all of the genes; the turquoise squares represent the coding density of orthologs between the genomes of A. orientalis and A. mediterranei; and the yellow circles represent the coding density of the essential genes. The area within the black square frame is the P2 region containing the vcm cluster, with a lower coding density of orthologs and essential genes. (B) Alignment of the P2 region with its flanking genes related to the vancomycin biosynthesis in selected actinomycete genomes. The green arrows represent the omitted genes in the corresponding genomes. (C) Alignment of the P1 region with its flanking genes related to the rifamycin biosynthesis in selected actinomycete genomes. All of the genome data are available at NCBI.