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  • Reference-grade genome and large linear plasmid of streptomyces rimosus: pushing the limits of nanopore sequencing [Elektronski vir]
    Slemc, Lucija ...
    Streptomyces rimosus ATCC 10970 is the parental strain of industrial strains used for the commercial production of the important antibiotic oxytetracycline. As an actinobacterium with a large linear ... chromosome containing numerous long repeat regions, high GC content, and a single giant linear plasmid (GLP), these genomes are challenging to assemble. Here, we apply a hybrid sequencing approach relying on the combination of short- and long-read next-generation sequencing platforms and whole-genome restriction analysis by using pulsed-field gel electrophoresis (PFGE) to produce a high-quality reference genome for this biotechnologically important bacterium. By using PFGE to separate and isolate plasmid DNA from chromosomal DNA, we successfully sequenced the GLP using Nanopore data alone. Using this approach, we compared the sequence of GLP in the parent strain ATCC 10970 with those found in two semi-industrial progenitor strains, R6-500 and M4018. Sequencing of the GLP of these three S. rimosus strains shed light on several rearrangements accompanied by transposase genes, suggesting that transposases play an important role in plasmid and genome plasticity in S. rimosus. The polished annotation of secondary metabolite biosynthetic pathways compared to metabolite analysis in the ATCC 10970 strain also refined our knowledge of the secondary metabolite arsenal of these strains. The proposed methodology is highly applicable to a variety of sequencing projects, as evidenced by the reliable assemblies obtained.
    Vir: Microbiology spectrum [Elektronski vir]. - ISSN 2165-0497 (Vol. 10, iss. 2, Mar./Apr. 2022, str. 1-20)
    Vrsta gradiva - e-članek ; neleposlovje za odrasle
    Leto - 2022
    Jezik - angleški
    COBISS.SI-ID - 103836931

    Povezava(-e):

    https://journals.asm.org/doi/10.1128/spectrum.02434-21
    DOI

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