Reference-Grade Genome and Large Linear Plasmid of Streptomyces rimosus: Pushing the Limits of Nanopore Sequencing-Reference-Cited by-同舟云学术

Reference-Grade Genome and Large Linear Plasmid of Streptomyces rimosus: Pushing the Limits of Nanopore Sequencing

Published:2022-04-27 Issue:2 Volume:10 Page:
ISSN:2165-0497
Container-title:Microbiology Spectrum
language:en
Short-container-title:Microbiol Spectr

Author:

Slemc Lucija¹,Jakše Jernej²^ORCID,Filisetti Alessandro³,Baranasic Damir⁴,Rodríguez-García Antonio⁵,Del Carratore Francesco⁶^ORCID,Marino Stefano Maria³^ORCID,Zucko Jurica⁴,Starcevic Antonio⁴,Šala Martin⁷,Pérez-Bonilla Mercedes⁸,Sánchez-Hidalgo Marina⁸^ORCID,González Ignacio⁸,Reyes Fernando⁸,Genilloud Olga⁸,Springthorpe Vicki⁹,Goranovič Dušan¹⁰,Kosec Gregor¹⁰,Thomas Gavin H.⁹^ORCID,Lucrezia Davide De³,Petković Hrvoje¹,Tome Miha¹^ORCID

Affiliation:

1. Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia

2. Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia

3. Explora Biotech Srl, Venice, Italy

4. Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia

5. INBIOTEC Instituto de Biotecnología de León, Parque Científico de la Granja, León, Spain

6. Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom

7. National Institute of Chemistry, Ljubljana, Slovenia

8. Fundación MEDINA, Parque Tecnológico Ciencias de la Salud, Granada, Spain

9. Department of Biology, University of York, York, United Kingdom

10. Acies Bio d.o.o., Ljubljana, Slovenia

Abstract

The genomes of Streptomyces species are difficult to assemble due to long repeats, extrachromosomal elements (giant linear plasmids [GLPs]), rearrangements, and high GC content. To improve the quality of the S. rimosus ATCC 10970 genome, producer of oxytetracycline, we validated the assembly of GLPs by applying a new approach to combine pulsed-field gel electrophoresis separation and GLP isolation and sequenced the isolated GLP with Oxford Nanopore technology.

Funder

Javna Agencija za Raziskovalno Dejavnost RS

Ministrstvo za Izobraževanje, Znanost in Šport

EC | European Regional Development Fund

EC | HORIZON EUROPE Framework Programme

Publisher

American Society for Microbiology

Subject

Infectious Diseases,Cell Biology,Microbiology (medical),Genetics,General Immunology and Microbiology,Ecology,Physiology

Link

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

Reference69 articles.