Compartir
Título
Reference-grade genome and large linear plasmid of Streptomyces rimosus: pushing the limits of Nanopore sequencing
Autor
Facultad/Centro
Área de conocimiento
Título de la revista
Microbiology Spectrum
Número de la revista
2
Cita Bibliográfica
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
Editorial
American Society for Microbiology (ASM)
Fecha
2022-04-04
Resumen
[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
Materia
Palabras clave
Peer review
SI
ID proyecto
- info:eu-repo/grantAgreement/EC/H2020/720793/EU
URI
DOI
Versión del editor
Aparece en las colecciones
- Artículos [5104]
Ficheros en el ítem
Tamaño:
1.546
xmlui.dri2xhtml.METS-1.0.size-megabytes
Formato:
Adobe PDF