Table 5.
Allelic profiles of the 33 Francisella isolates used in the study.
| Allelic profile | Strain name | Fnn-VNTR1 | Fnn-VNTR2 | Fnn-VNTR3 | Fnn-VNTR4 | Fnn-VNTR5 | Fnn-VNTR6 | Fnn-VNTR7 |
|---|---|---|---|---|---|---|---|---|
| F. noatunensis ssp. Noatunensis | ||||||||
| FnnUA2660A | NA | 392nt - 33r | 212nt - 10r | 335nt - 14br | 285nt - 2r | 307nt - 12hr | 405nt - 2ir | |
| I | FnnR-001 -04 (GM2212) T | 211nt - 7r | 217nt - 8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| I | FnnR-002 - 06 | 211nt - 7r | 217nt -8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| I | FnnR-004 - 06 | 211nt - 7r | 217nt - 8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| I | FnnR-017 - 05 | 211nt - 7r | 217nt - 8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| I | FnnMR-005 - 06 | 211nt - 7r | 217nt - 8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| I | FnnMR-011 - 07 | 211nt - 7r | 217nt -8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| I | FnnSF-012 - 07 | 211nt - 7r | 217nt - 8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| I | FnnMR-013 - 07 | 211nt - 7r | 217nt - 8r | 212nt - 10r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| II | FnnR-003 - 06W | 211nt - 7r | 217nt - 8r | 207nt - 9r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r |
| II | FnnN-006 - 06 | 211nt - 7r | 217nt - 8r | 207nt - 9r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt- 5r |
| III | FnnH-007 - 06 F | 219nt - 8r | 259nt - 14r | 202nt - 8r | 341nt - 15r | 312nt - 5r | 301nt - 10er | 430nt - 4r |
| III | NCIMB 14265T | 219nt - 8r | 259nt - 14r | 202nt - 8r | 341nt - 15r | 312nt - 5r | 301nt - 10er | 430nt - 4r |
| III | FnnH-014 - 06F | 219nt - 8r | 259nt - 14r | 202nt - 8r | 341nt - 15r | 312nt - 5r | 301nt - 10er | 430nt - 4r |
| III | FnnSF-018 - 09 | 219nt - 8r | 259nt- 14r | 202nt - 8r | 341nt - 15r | 312nt - 5r | 301nt - 10er | 430nt- 4r |
| III | FnnSF-019 - 09 | 219nt - 8r | 259nt - 14r | 202nt - 8r | 341nt - 15r | 312nt - 5r | 301nt - 10er | 430nt - 4r |
| FnnH-008 - 06W | 195nt - 5r | 217nt - 8r | 202nt - 8r | 311nt - 10r | 312nt - 5r | 301nt - 10er | 435nt - 5r | |
| FnnMR-015 - 08F | 195nt - 5r | 259nt - 14r | 197nt - 7r | 437nt - 31r | 312nt - 5r | 301nt - 10er | 435nt - 5r | |
| FnnH-016 - 08F | 219nt - 8r | 287nt - 18r | 197nt - 7r | 359nt - 18r | 312nt- 5r | 295nt - 8er | 435nt - 5r | |
| FnnAA-009 - 07W | 211nt - 7r | 294nt - 19r | 197nt - 7r | 347nt - 16r | 312nt - 5r | 301nt - 10er | 435nt - 5r | |
| FnnVA-010 - 07W | 211nt - 7r | 308nt - 21r | 197nt - 7r | 329nt - 13r | 312nt - 5r | 301nt - 10er | 435nt - 5r | |
| FnnH-020 - 09 | 195nt - 5r | 280nt - 17r | 207nt - 9r | 437nt - 31r | 312nt - 5r | 301nt - 10er | 435nt - 5r | |
| F. noatunensis ssp. orientalis | ||||||||
| FnoJ-001 - 02 (Ehime-1) | 195nt - 5r | 217nt - 8r | NA | 317nt - 11dr | 285nt - 2r | 301nt - 10fr | 405nt - 2ir | |
| FnoI-002 - 04 1368 | 211nt - 7r | 392nt - 33r | 212nt - 10r | 365nt - 19dr | 285nt - 2r | 301nt - 10fr | 404nt - 1.8r | |
| FnoI-003 - 05 1436 | 211nt - 7r | 217nt - 8r | 212nt - 10r | 329nt - 13dr | 285nt - 2r | 301nt - 10fr | 404nt - 1.8r | |
| FnoI-004 - 07 2070 | 211nt - 7r | 217nt - 8r | 212nt- 10r | 371nt - 20dr | 285nt - 2r | 301nt - 10fr | 404nt - 1.8r | |
| F. philomiragia | ||||||||
| FpDSM7535T | NA | 175nt - 2.8br | 182nt - 4c | 401nt - 25dr | NA | 301nt - 10gr | 404nt - 1.8r | |
| FpCCUG19701 | NA | 175nt - 2.8br | NA | 395nt - 24dr | NA | 301nt - 10gr | 405nt - 2r | |
| FpCCUG13404 | NA | 175nt - 2.8br | NA | 311nt - 10dr | NA | 301nt - 10gr | 404nt - 1.8r | |
| FpCCUG12603 | NA | 175nt - 2.8br | NA | 407nt - 26dr | NA | 301nt - 10gr | 425nt - 3r | |
| Fp1951 | NA | 175nt - 2.8ar | NA | 443nt - 32r | NA | 301nt - 10gr | 404nt - 1.8r | |
| Fp080107 -I | NA | Na | NA | 431nt - 30dr | NA | 301nt - 10gr | 405nt - 2r | |
| Fp080107 -II | NA | 175nt - 2.8ar | NA | 257nt - 1ar | NA | 301nt - 10gr | 404nt - 1.8r | |
Identical allelic profiles are assigned Greek numerals I-III. Allelic profiles are presented as number of nucleotides in repeat marker (nt) and numbers of repeats (r). Identical profiles occur for several isolates from cod culturing, profile I (FnnR-001-04 to FnnMR-013-07), profile II (FnnR-003-06W and FnnN-006-06) and profile III (FnnH-007-06 to FnnSF-019-09)
Isolated in ChileA, Isolated from broodfishF, type strainT, W = wild caught, NA = Not Amplified with primer sets
Heterogeneous repeats with Single Nucleotide Polymorphism (snp), noted as nucleotide number in repeat sequence (nt) and at repeat of occurrence (r); a = snp G-A nt1 r1 r3 b = snp. G-A nt1 r3, c = snp G-A nt3 r4, d = snp T-C nt1 from r2, e = 2 snp C-T nt1 r4 r6, f = 2 snp C-T nt1 r5 r7, g = 2 snp C-T nt1 r6 r8, h = 2 snp C-T nt1 r8 r10, i = snp T-C nt4 r1