TABLE 1.
Strain and lineage genomic differences linked to phenotypic variabilitya.
| Gene or Island | Lineage I | Lineage II | Lineage III |
| LIPI-1b | (1) 27/28 | (3) 21/24 | 4/4 |
| LIPI-3c | (2) 20/28 | 0/24 | 0/4 |
| LIPI-4 | 6/28 | 0/24 | 0/4 |
| inlA | 28/28 | 14/24 | 4/4 |
| inlB | 27/28 | 24/24 | 4/4 |
| SSI-1 | 3/28 | 15/24 | 3/4 |
| cspA, cspB, cspD | 28/28 | 24/24 | 4/4 |
| BC resistance genes | 1/28 | 4/24 | 0/4 |
| lmo1080-1084 cassetted | 3/28 | (2) 24/24 | 0/4 |
aOnly a few selected genomic differences are presented. For more details, refer to Supplementary Tables 2, 3.
b(1) 27/28 means 27 of 28 LI strains have a LIPI-1 with all full-length proteins, whereas 1 strain has at least one truncated LIPI-1 protein. LI strain H34 encodes a truncated PlcB, whereas LII strains (N843_10, N843_15, and N05-195) encode a truncated PrfA.
cTwo of 20 strains encoded truncated proteins, strain N11-2747 has a truncated IisP, whereas N13-2107, a CC4 strain, has a truncated IisX.
dTwo of 24 strains encoded truncated proteins, strain N843_10 and N843_15 encode truncated RmlB (Lmo1083) proteins.