High quality genome annotation and expression visualisation of a mupirocin-producing bacterium

Area of Science:

• Microbiology
• Genomics
• Metabolic Engineering

Background:

• Pseudomonas strain NCIMB10586 produces the polyketide antibiotic mupirocin.
• This strain shows potential for industrial production of valuable compounds.
• High-quality genome sequencing and annotation are crucial for further research.

Purpose of the Study:

• To generate a high-quality genome sequence and annotation for Pseudomonas NCIMB10586.
• To investigate the genetic and physiological characteristics of the strain.
• To facilitate studies on mupirocin production and other industrial applications.

Main Methods:

• Hybrid genome assembly using Illumina and PacBio reads.
• Combined automated and manual annotation pipeline.
• RNA sequencing (RNAseq) analysis over an 18-hour growth period.

Main Results:

• A high-quality genome assembly was achieved, correcting 415 sequencing errors.
• The annotation pipeline improved the accuracy of coding region identification.
• RNAseq analysis revealed coordinated expression of the mupirocin cluster and constitutive expression of a resistance gene.

Conclusions:

• The enhanced genome sequence and annotation provide a valuable resource for Pseudomonas NCIMB10586 research.
• The findings support the strain's potential for industrial applications, including antibiotic production.
• The study presents novel methods for genome assembly, annotation, and RNAseq data analysis.