A panoramic view of the genomic landscape of the genus Streptomyces

We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species -level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon dem-onstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus -level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species -level fingerprints, smBGCs, CAZymes and TTA- codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.

Automated summary

We studied the genomes of 213 Streptomyces species and found high levels of internal homology and complexity in their last common ancestor. Species-specific fingerprint proteins were identified, showing high interspecies variability. Chromosomal protein-coding genes, core genes, accessory genes, and fingerprints all exhibited significant variability even among closely related species. The chromosome arms were found to be responsible for rapid adaptation at the species and strain level, while the total number of CAZymes showed a moderate correlation with certain types of smBGCs related to bacterial competition.