TABLE 1.
Phylogenetic resolution of primer 8-27f TRFs predicted for different enzymes
| Enzyme(s) | Divisiona | No. of TRFs | TRFs between 94 and 827 bpc | % Species-specific TRFsd | % Species- or genus-specific TRFsd | % Species- or genus-specific binse |
|---|---|---|---|---|---|---|
| HaeIII | G+, Proteo | 228 (2,025b) | 182 (1,442b) | 46 (11f) | 50 (15f) | 19 (7f) |
| BstUI | G+, Proteo | 358 (2,015) | 290 (1,706) | 63 (15) | 70 (24) | 42 (11) |
| HhaI | G+, Proteo | 406 (2,021) | 294 (1,607) | 62 (15) | 70 (21) | 37 (6) |
| MspI | G+, Proteo | 311 (2,007) | 276 (1,836) | 61 (13) | 70 (16) | 34 (9) |
| RsaI | G+, Proteo | 354 (2,015) | 266 (1,489) | 68 (23) | 70 (31) | 43 (15) |
| HaeIII | G+ | 183 (1,089) | 164 (927) | 61 (27) | 64 (32) | 22 (8) |
| BstUI | G+ | 197 (1,090) | 179 (1,036) | 65 (23) | 69 (28) | 50 (18) |
| HhaI | G+ | 305 (1,089) | 226 (901) | 68 (30) | 76 (42) | 46 (21) |
| MspI | G+ | 220 (1,081) | 200 (1,011) | 66 (28) | 72 (38) | 44 (19) |
| RsaI | G+ | 244 (1,090) | 185 (819) | 75 (30) | 77 (33) | 59 (24) |
| HaeIII + RsaI | G+ | 217 (1,086) | 194 (888) | 69 (35) | 74 (45) | NDg |
| BstUI + RsaI | G+ | 212 (1,088) | 184 (880) | 70 (31) | 74 (39) | ND |
| HhaI + RsaI | G+ | 286 (1,086) | 251 (867) | 73 (42) | 81 (61) | ND |
| MspI + RsaI | G+ | 228 (1,079) | 202 (860) | 70 (36) | 50 (76) | ND |
| HaeIII | Proteo | 133 (936) | 97 (515) | 63 (23) | 70 (34) | 36 (17) |
| BstUI | Proteo | 129 (935) | 120 (886) | 61 (13) | 66 (18) | 44 (10) |
| HhaI | Proteo | 176 (926) | 128 (705) | 67 (22) | 72 (28) | 47 (14) |
| MspI | Proteo | 165 (926) | 141 (825) | 67 (20) | 73 (30) | 40 (16) |
| RsaI | Proteo | 200 (925) | 148 (670) | 73 (29) | 77 (36) | 53 (23) |
| HaeIII + RsaI | Proteo | 146 (936) | 122 (519) | 70 (32) | 75 (42) | ND |
| BstUI + RsaI | Proteo | 142 (935) | 125 (866) | 61 (14) | 66 (21) | ND |
| HhaI + RsaI | Proteo | 186 (932) | 157 (755) | 69 (24) | 77 (33) | ND |
| MspI + RsaI | Proteo | 190 (926) | 165 (809) | 67 (26) | 70 (35) | ND |
G+, gram positive; Proteo, Proteobacteria.
Number of sequences represented by the TRFs.
The range was derived from the Genescan 2500 size standard (ABI) that was used for determination of fragment sizes in gel electrophoresis.
Only the specificity of TRFs in the analysis range (94 to 827 bp) was examined. A species-specific TRF was defined as a TRF size representing strains from three or fewer species, and each TRF size representing strains from two or fewer genera was counted as a genus-specific TRF. The listed values are percentages of the numbers of TRFs between 94 and 827 bp (from column 4).
Each bin consisted of a TRF size of ±1 bp.
Percentages of sequences (from the totals in column 4) that were represented by phylogenetically specific TRFs.
ND, not determined.