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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