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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