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Table 4 CRISPR-Cas systems identified in the studied strains by CRISPR-finder

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

Strain

Predicted CRISPR

Start

End

Size

DR (nt)

No. spacers

Type

Immunity to identified phages

Immunity to mobile elements identified in this study

Locus ID

Note

JS

Crispr_2

2,424,099

2,427,021

2922

36

40

IU

Anatole, B3, B22, E1, E6, G4, PFR1, PFR2

PJS22, PJS23, PJS7, pJS12

PFREUDJS001_002141-PFREUDJS001_002147

–

JS2

Crispr_3

2,082,550

2,088,376

5826

28

95

IE

B22, B3, E1,E6, G4, Anatole, Doucette, PFR1, PFR2

PJS22, PJS23, PJS7, pJS25

PFR_JS2_1825-PFR_JS2_1832

–

Crispr_4

2,120,759

2,122,610

1851

36

25

IU

PFR1, PFR2

PJS7

PFR_JS2_1843-PFR_JS2_1849

–

JS4

Crispr_3

1,825,170

1,827,746

2576

36

35

IU

Doucette, E6, G4, PFR1, PFR2

PJS22, PJS7, pJS25

PFR_JS4_1650-PFR_JS4_1655

One system, negative strand, spacers separated by a transposase gene and then by a four-gene integron.

Crispr_2

1,823,162

1,823,697

535

36

7

 

–

–

 

Crispr_1

1,818,598

1,819,215

617

36

8

 

–

–

 

JS7

Crispr_2

2,203,337

2,207,335

3998

28

65

IE

B22, B3, E1,E6, G4, Anatole, Doucette, PFR1, PFR2

PJS22, PJS7, pJS12

PFR_JS7–1_1964-PFR_JS7–1_1971

No cas2

JS8

Crispr_3

2,192,257

2,196,491

4234

36

58

IU

Anatole, Doucette, B3, B22, E1, E6, G4, PFR1, PFR2, phiB5

PJS22, PJS23, PJS7, pJS25

PFR_JS8_1930-PFR_JS8_1935

–

JS9

Crispr_3

2,260,079

2,260,655

576

28

9

IE

–

–

PFR_JS9–1_2018-PFR_JS9–1_2025

One system, negative strand, spacers separated by an integrase

Crispr_2

2,253,046

2,258,937

5891

28

96

 

B22, B3, E1,E6, G4, Anatole, Doucette, PFR1, PFR2, phiB5

–

 

Crispr_4

2,288,755

2,292,746

3991

29

65

N/A

Doucette, B3, B22, G4, PFR1, PFR2

PJS23, PJS7

 

Remnant of a system, no Cas. Spacers separated by an integrase.

Crispr_5

2,293,887

2,295,016

1129

29

18

 

PFR1, PFR2

PJS7

 

JS10

Crispr_2

2,029,533

2,032,236

2703

36

37

IU

Anatole, B3, B22, E1, E6, G4, PFR1, PFR2

PJS22, PJS23, PJS7, pJS12

PFR_JS10_1797-PFR_JS10_1803

 

JS12

Crispr_1

2,181,462

2,185,411

3949

36

54

IU

Doucette, B3, B22, E6, G4, PFR1, PFR2, phiB5

PJS22, PJS23, PJS7

PFR_JS12–1_1906-PFR_JS12–1_1911

 

JS14

PossibleCrispr_1

1,595,184

1,595,290

106

36

1

N/A

Anatole, E1

 

PFR_JS14_1397

 

JS15_1

Crispr_1

441,841

444,266

2425

36

33

IU

Anatole, B3, B22, E1, E6, G4, phiB5

PJS23, pJS12

PFR_JS15–1_371-PFR_JS15–1_376

 

JS16

Crispr_2

417,820

419,522

1702

36

23

IU

B22, E6, G4, PFR1, PFR2

PJS22, PJS23, PJS7

RM25_0342-RM25_0347

One system, negative strand, spacers separated by a transposase gene. Both CRISPR stretches carry immunity to known phages.

Crispr_1

413,342

416,347

3005

36

41

 

Anatole, B3, B22, E1, E6

PJS22

 

JS17_1

Crispr_2

2,220,735

2,225,402

4667

36

64

IU

Anatole, Doucette, B3, B22, E1, PFR1, PFR2

PJS22, PJS23, pJS12, pJS25

PFR_JS17–1_1953-PFR_JS17–1_1958

–

JS20_1

Crispr_3

2,034,463

2,037,183

2720

36

37

IU

Doucette, B22, E6, G4, PFR1, PFR2

PJS23, PJS7

PFR_JS20–1_1815-PFR_JS20–1_1820

One system, spacers separated by a transposase gene and then by an eight-gene integron.

Crispr_4

2,038,656

2,039,048

392

36

5

 

–

–

 

Crispr_5

2,044,247

2,044,936

689

36

9

 

–

–

 

JS21_1

Crispr_5

2,189,758

2,192,624

2866

36

39

IU

Doucette, E6, G4, PFR1, PFR2

PJS22, PJS7, pJS25

PFR_JS21–1_1963-PFR_JS21–1_1968

One system, negative strand, the spacers separated by a transposase gene and then by a four-gene integron.

Crispr_4

2,187,750

2,188,285

535

36

7

 

–

–

 

Crispr_3

2,183,185

2,183,803

618

36

8

 

–

–

 

JS22

Crispr_2

2,150,779

2,151,318

539

36

7

IU

–

–

 

Remnant of the same IU system, but no Cas. No immunity to known phages found.

JS23

Crispr_2

2,124,520

2,126,512

1992

36

27

IU

Anatole, B3, B22, E1, E6, G4, phiB5

PJS23

PFR_JS23_1889-PFR_JS23_1894

–

JS25

Crispr_2

2,042,081

2,045,018

2937

36

40

IU

Doucette, E6, PFR1, PFR2

PJS22,PJS7,pJS25

PFR_JS25–1_1807-PFR_JS25–1_1812

One system, spacers separated by a transposase gene and then by a four-gene integron.

Crispr_3

2,046,491

2,046,954

463

36

6

 

–

–

 

Crispr_4

2,050,901

2,051,519

618

36

8

 

–

–

 
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BMC Genomics

ISSN: 1471-2164

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