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

BMC Genomics

Research Article

Vieno Piironen¹  Kirsi Savijoki¹  Pekka Varmanen¹  Paulina Deptula¹  Helena Vihinen²  Petri Auvinen²  Olli-Pekka Smolander²  Lars Paulin²  Eija Jokitalo²  Pia K. Laine²  Richard J. Roberts³ 

[1] Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland;Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland;New England Biolabs, 01938-2723, Ipswich, MA, USA;

关键词: Propionibacterium freudenreichii;    Comparative genomics;    Bacteriophage;    Pilus;    Vitamin B12;    PacBio;    Complete genome;    Mobile elements;    Restriction and modification;    CRISPR-Cas;    Gras;   

DOI  :  10.1186/s12864-017-4165-9

 received in 2017-06-07, accepted in 2017-10-05,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundPropionibacterium 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.ResultsWe 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.ConclusionThe 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.

【 授权许可】

CC BY   
© The Author(s). 2017