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Table 3 P. freudenreichii strains included in this study. The details of differences between the genome sequences within strains

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

Strain Accession number GC% Note Details
JS7 LT618776 67% Genome with prophage PFR_JS7–1_1810 HTH-type transcriptional regulator KmtR:PFR_JS7–1_1869 Transcriptional regulator MtrR (preceeded by tRNA-Lys)
LT618777 67% Genome without phage  
JS9 LT618785 67% Genome with an additional transposase gene PFR_JS9–1_62 Uma4 protein
LT618786 67%   
JS12 LT604998 67% Genome with an additional transposase gene PFR_JS12–1_615 a Transposase of ISAar20, ISL3 family and PFR_JS12–1_616 Hypothetical protein (ahead of Carbon starvation protein)
LT576787 67%   
JS13 LT618779 67% Genome with 11-gene insertion or deletion b JS13_289 Hypothetical protein: JS13_299 Transposase for insertion sequence element IS1001
LT618780 67%   
JS15 LT618787 67% 3 transposase genes absent from the other genome PFR_JS15–1_878 Uma4 protein and PFR_JS15–1_879 Hypothetical protein; PFR_JS15–1_1737 Transposase of ISAar20, ISL3 family (Transposase gene disrupting gene coding for CitT); PFR_JS15–1_2045 a Transposase of ISAar20, ISL3 family
LT618788 67% Transposase gene disrupting a Type III restriction enzyme PFR_JS15–2_359 Transposase of ISAar43,IS3 family, IS407 group, orfA and PFR_JS15–2_360 c Insertion sequence IS407 orfB
JS17 LT618789 67% A duplicated transposase gene PFR_JS17–1_657 and PFR_JS17–1_658 a Transposase of ISAar20, ISL3 family
LT618790 67%   
JS20 LT618792 67% 3 transposase genes absent from the other genome PFR_JS20–2_544 Insertion sequence IS407 OrfB and PFR_JS20–2_545 c Transposase of ISAar43,IS3 family, IS407 group, orfA (disrupting Transposase IS30 family gene); PFR_JS20–2_568 Transposase of ISAar20, ISL3 family (ahead of Carbon starvation protein); PFR_JS20–2_1234 Transposase of ISAar20, ISL3 family (ahead of LuxS)
LT618791 67%   
JS21 LT618781 67% Transposase gene ahead of putative aminotransferase biotin synthesis related protein PFR_JS21–2_248 Transposase of ISAar20, ISL3 family
LT618782 67%   
  1. a Transposase genes PFR_JS12–1_615, PFR_JS15–1_2045, PFR_JS17–1_657 and PFR_JS17–1_658 found in strains JS12, JS15 and JS17, respectively, are 100% identical
  2. b The same element is present in the strain JS11 in the same location, but in all of the sequences
  3. c Transposase genes PFR_JS15–2_359 and PFR_JS15–2_360 are identical to PFR_JS20–2_544 and PFR_JS20–2_545. The transposase genes do not appear to be acquired through horisontal transfer, as each of them is present in their respective genomes in at least one more location. All of the transposase genes have counterparts in multiple strains, suggesting their intrinsic character for the species