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

Show full item record



Permalink

http://hdl.handle.net/10138/231312

Citation

Deptula , P , Laine , P K , Roberts , R J , Smolander , O-P , Vihinen , H , Piironen , V , Paulin , L , Jokitalo , E , Savijoki , K , Auvinen , P & Varmanen , P 2017 , ' De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii ' , BMC Genomics , vol. 18 , 790 . https://doi.org/10.1186/s12864-017-4165-9

Title: De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii
Author: Deptula, Paulina; Laine, Pia K.; Roberts, Richard J.; Smolander, Olli-Pekka; Vihinen, Helena; Piironen, Vieno; Paulin, Lars; Jokitalo, Eija; Savijoki, Kirsi; Auvinen, Petri; Varmanen, Pekka
Other contributor: University of Helsinki, Department of Food and Nutrition
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Food and Nutrition
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Food and Nutrition
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Food and Nutrition







Date: 2017-10-16
Language: eng
Number of pages: 24
Belongs to series: BMC Genomics
ISSN: 1471-2164
DOI: https://doi.org/10.1186/s12864-017-4165-9
URI: http://hdl.handle.net/10138/231312
Abstract: Background: 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.
Subject: Propionibacterium freudenreichii
Comparative genomics
Bacteriophage
Pilus
Vitamin B12
PacBio
Complete genome
Mobile elements
Restriction and modification
CRISPR-Cas
Gras
CHAIN FATTY-ACIDS
SSP SHERMANII JS
ANTIINFLAMMATORY PROPERTIES
PROKARYOTIC GENOMES
ADAPTIVE IMMUNITY
INTESTINAL MUCUS
BACTERIA
TOOL
METABOLISM
INSIGHTS
1183 Plant biology, microbiology, virology
1184 Genetics, developmental biology, physiology
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
s12864_017_4165_9.pdf 3.739Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record