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A panoramic view of the genomic landscape of the genus Streptomyces
Nikolaidis, Marios; Hesketh, Andrew; Frangou, Nikoletta; Mossialos, Dimitris; Van de Peer, Yves; Oliver, Stephen G.; Amoutzias, Grigorios D.
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 demonstrate
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.