RT info:eu-repo/semantics/article
T1 Reference-grade genome and large linear plasmid of Streptomyces rimosus: pushing the limits of Nanopore sequencing
A1 Slemc, Lucija
A1 Jakše, Jernej
A1 Filisetti, Alessandro
A1 Baranasic, Damir
A1 Rodríguez García, Antonio
A1 Del Carratore, Francesco
A1 Marino, Stefano Maria
A1 Zucko, Jurica
A1 Starcevic, Antonio
A1 Šala, Martin
A1 Pérez-Bonilla, Mercedes
A1 Sánchez-Hidalgo, Marina
A1 González, Ignacio
A1 Reyes, Fernando
A1 Genilloud, Olga
A1 Springthorpe, Vicki
A1 Goranovič, Dušan
A1 Kosec, Gregor
A1 Thomas, Gavin H.
A1 Lucrezia, Davide De
A1 Petković, Hrvoje
A1 Tome, Miha
A2 Microbiologia
K1 Biología
K1 Biotecnología
K1 Streptomyces rimosus genome
K1 Linear plasmid
K1 Nanopore sequencing
K1 Reference genome
K1 Biosynthetic gene clusters
K1 Oxytetracycline
K1 Pulsed-field electrophoresis
K1 Transposase
K1 2415.01 Biología Molecular de Microorganismos
AB [EN] 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
PB American Society for Microbiology (ASM)
LK https://hdl.handle.net/10612/18100
UL https://hdl.handle.net/10612/18100
NO Slemc, L., Jakše, J., Filisetti, A., Baranasic, D., Rodríguez-García, A., Carratore, F. D., Marino, S. M., Zucko, J., Starcevic, A., Šala, M., Pérez-Bonilla, M., Sánchez-Hidalgo, M., González, I., Reyes, F., Genilloud, O., Springthorpe, V., Goranovič, D., Kosec, G., Thomas, G. H., et al. (2022). Reference-grade genome and large linear plasmid of Streptomyces rimosus: pushing the limits of Nanopore sequencing. Microbiology Spectrum, 10(2), Article e2434. https://doi.org/10.1128/SPECTRUM.02434-21
DS BULERIA. Repositorio Institucional de la Universidad de León
RD 12-jun-2024