Data from: De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

Back to summary metadata
dc.contributor.affiliationUniversity of Helsinki-Varmanen, Pekka
dc.contributor.authorVarmanen, Pekka
dc.date.accessioned2025-04-29T14:00:01Z
dc.date.issued2018-10-05
dc.date.issued2018-10-05
dc.descriptionBackground: Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species. Results: We used the PacBio RS II sequencing platform to generate complete genomes of 20 P. freudenreichii strains and compared them in detail. Comparative analyses revealed both sequence conservation and genome organisational diversity among the strains. Assembly from long reads resulted in the discovery of additional circular elements: two putative conjugative plasmids and three active, lysogenic bacteriophages. It also permitted characterisation of the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed identification of DNA modifications, which in turn allowed characterisation of the restriction-modification systems together with their recognition motifs. The observed genomic differences suggested strain variation in surface piliation and specific mucus binding, which were validated by experimental studies. The phenotypic characterisation displayed large diversity between the strains in ability to utilise a range of carbohydrates, to grow at unfavourable conditions and to form a biofilm. Conclusion: The complete genome sequencing allowed detailed characterisation of the industrially important species, P. freudenreichii by facilitating the discovery of previously unknown features. The results presented here lay a solid foundation for future genetic and functional genomic investigations of this actinobacterial species.
dc.identifierhttps://doi.org/10.5061/dryad.kg5s5
dc.identifier.urihttps://datakatalogi.helsinki.fi/handle/123456789/4589
dc.rights.licensecc-zero
dc.subjectCRISPR-Cas
dc.subjectpilus
dc.subjectvitamin B12
dc.subjectmobile elements
dc.subjectrestriction and modification
dc.subjectPropionibacterium freudenreichii
dc.subjectComplete genome
dc.subjectGRAS
dc.subjectBacteriophage
dc.subjectComparative genomics
dc.subjectPacBio
dc.titleData from: De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii
dc.typedataset

Files

Repositories

Zenodo