A treasure trove of 1034 actinomycete genomes

This paper report the whole genome sequencing of 1034 Actinomycetia strains from the New Bioactive Compounds (NBC) Collection of the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark; 881 strains with complete genomes and 153 near-complete genomes.

Abstract

Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.

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Recommended citation: TS Jørgensen, OS Mohite, EB Sterndorff, M Alvarez-Arevalo, K Blin, TJ Booth, P Charusanti, D Faurdal, TØ Hansen, **M Nuhamunada**, A Mourched, BØ Palsson, T Weber, A treasure trove of 1034 actinomycete genomes, Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7487–7503.
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