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

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. In the current project we report complete genome sequences of 17 additional P. freudenreichii strains and a re-sequenced whole genome of the strain DSM 4902 (JS15) generated with the PacBio RSII sequencing platform. We assembled 31 complete and circular sequences from the eighteen strains. For 11 of the strains, assembly from long reads resulted in more than one genome. In five of the strains circular elements were found: in JS12 and JS25 putative conjugative plasmids and in JS7, JS22 and JS23 bacteriophage genomes. In eight of the strains, the additional genomes resulted from duplication and relocation (copy and paste) of transposable elements. The accession numbers of the differing genomes are listed below: JS7: LT618776 Genome with prophage LT618777 Genome without phage LT618778 Circular phage JS9: LT618785 Genome with an additional transposase gene LT618786 JS12: LT604998 Genome with an additional transposase gene LT576787 LT604882 Putative conjugative plasmid JS13: LT618779 Genome with an 11-gene insertion LT618780 JS15: LT618787 Genome with 3 additional transposase genes LT618788 Genome with a transposase gene disrupting a Type III RM methylase JS17: LT618789 Genome with a duplicated transposase gene LT618790 JS20: LT618791 LT618792 Genome with 3 additional transposase genes JS21: LT618781 Genome with additional transposase genes LT618782 JS22: LT599498 Genome with prophage LT615138 Circular phage JS23: LT618793 Genome with prophage LT618794 Circular phage JS25: LT618783 LT618784 Putative conjugative plasmid