Table 1.
Genomic mutations of the three R20291 stocks compared with the reference genome sequence.
| Position | Gene | Locus Tag | Type | Reference ID | Mutated ID | AA substitution |
|---|---|---|---|---|---|---|
| [1] Common to all three strains | ||||||
| 132924 | met-tRNA | Insertion | – | A | ||
| 132939 | met-tRNA | SNP | G | T | ||
| 132955 | met-tRNA | SNP | C | A | ||
| 132958–59 | met-tRNA | SNP | TT | CG | ||
| 143463 | Intergenic | Insertion | – | A | ||
| 206399 | Intergenic | Insertion | – | A | ||
| 581481 | Intergenic | Insertion | – | A | ||
| 581488 | Intergenic | Insertion | – | A | ||
| 581495 | Intergenic | Insertion | – | A | ||
| 1564432 | Intergenic | Deletion | A | – | ||
| 1568676 | Ruberythrin | CDR20291_1323 | SNP | C | A | Gln138Lys |
| 1578167 | Intergenic | Deletion | T | – | ||
| 1578203 | Intergenic | Insertion | – | A | ||
| 1592813 | Intergenic | SNP | A | T | ||
| 1864417 | Pseudogene | CDR20291_1576 | Insertion | – | T | Ser7Frameshift∗ |
| 1899596 | Intergenic | Deletion | A | – | ||
| 2235738 | Membrane protein | CDR20291_1913 | Deletion | T | – | Val83Frameshift |
| 2262060 | Intergenic | Insertion | – | A | ||
| 2264190 | Intergenic | Deletion | T | – | ||
| 2298111 | Intergenic | Insertion | – | T | ||
| 2361948 | Intergenic | SNP | C | A | ||
| 2361957 | Intergenic | Insertion | – | A | ||
| 2367942 | Intergenic | Insertion | – | T | ||
| 2578157 | Intergenic | Deletion | T | – | ||
| 2674744 | Intergenic | Deletion | T | – | ||
| 2680787 | Intergenic | Insertion | – | T | ||
| 2772179 | Pseudogene∗∗ | CDR20291_2368 | Deletion | T | – | |
| 3077986 | Intergenic | Deletion | A | – | ||
| 3162098 | Intergenic | Deletion | T | – | ||
| 3361915 | Intergenic | Deletion | A | – | ||
| [2] Specific to CRG0825 | ||||||
| 9694 | rsbW | CDR20291_3551 | SNP | G | T | Gly82Val |
| 358260 | rbsK | CDR20291_0302 | Deletion | A | – | Met57Stop |
| 2077305 | Intergenic | (CDR20291_1777 to CDR20291_1778) | Deletion | C | – | |
| 2120669 | vncR | CDR20291_1806 | SNP | A | G | Asp202Gly |
| 2881467 | TCS-HK∗∗∗ | CDR20291_2456 | Deletion | T | – | Leu434Stop |
| [3] Specific to CRG3661 | ||||||
| 1340128 | codY | CDR20291_1115 | SNP | T | A | Try146Asn |
| 3292465 | gntR regulator | CDR20291_2781 | SNP | T | C | Ile58Met |
| 3472928 | Intergenic | (CDR20291_2929 to CDR20291_2928) | SNP | G | A | |
The region encompassing the mutation was aligned with multiple C. difficile genome sequences using NCBI Blastn. ∗Insertion here results in a frameshift mutation to a full-length pseudogene encoding an 87 AA protein. This gene without mutation encodes only 6 AAs. ∗∗Putative competence membrane protein ∗∗∗TCS-HC: Two-component system histidine kinase. The gene resides immediately downstream of an adjacent gene (CDR20291_2457) encoding a putative response regulator.