Abstract
Streptomyces are Gram-positive bacteria of significant industrial importance due to their ability to produce a wide range of antibiotics and bioactive secondary metabolites. Recent advances in genome mining have revealed that Streptomyces genomes possess a large number of unexplored silent secondary metabolite biosynthetic gene clusters (smBGCs). This indicates that Streptomyces genomes continue to be an invaluable source for new drug discovery. Here, we present high-quality genome sequences of 22 Streptomyces species and eight different Streptomyces venezuelae strains assembled by a hybrid strategy exploiting both long-read and short-read genome sequencing methods. The assembled genomes have more than 97.4% gene space completeness and total lengths ranging from 6.7 to 10.1 Mbp. Their annotation identified 7,000 protein coding genes, 20 rRNAs, and 68 tRNAs on average. In silico prediction of smBGCs identified a total of 922 clusters, including many clusters whose products are unknown. We anticipate that the availability of these genomes will accelerate discovery of novel secondary metabolites from Streptomyces and elucidate complex smBGC regulation.
Highlights
Background & SummaryWith the rapid emergence of antibiotic microbial resistance (AMR) to all major classes of antibiotics and the decline in number of potential candidates for new antibiotics, there is a pressing need for the discovery of novel antibacterial compounds[1]
Drug discovery from Streptomyces has been based on bioactivity screening followed by mass spectrometry and NMR-based molecular identification[5]
Recent advances in genomics-based approaches revealed that most of the secondary metabolite biosynthetic gene clusters of streptomycetes are inactive under laboratory conditions, suggesting that the ability of streptomycetes to produce secondary metabolites has been under-estimated[5,6]
Summary
Background & SummaryWith the rapid emergence of antibiotic microbial resistance (AMR) to all major classes of antibiotics and the decline in number of potential candidates for new antibiotics, there is a pressing need for the discovery of novel antibacterial compounds[1]. Accurate gene annotations based on high quality genome sequences are essential for the precise identification of smBGCs10. Gene annotation with the high quality genome of S. clavuligerus revealed that 30% out of a total High quality genome sequences are essential for multi-omics analysis, which facilitates the understanding of the complex regulation on smBGCs and rational engineering for increasing secondary metabolites production[11,12].
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