Table 3.
Characteristics of loci for S. mutans isolates using Nakano and Do MLST typing schemes.a
| Nakano scheme | ||||||||
| Locus | Fragment size (bp)b | No. of alleles | G + C Mol | No. polymorphic sites (%) | Synonymous changes | Non-synonymous changes | dN/dS | Tajima's D test |
| murI | 425 | 8 | 0.393 | 11 (2.59) | 8 | 3 | 0.054 | 0.302 |
| glnA | 460 | 8 | 0.378 | 7 (1.52) | 7 | 0 | 0 | −0.491 |
| tkt | 435 | 10 | 0.449 | 11 (2.53) | 10 | 1 | 0.043 | −0.976 |
| gyrA | 435 | 6 | 0.425 | 6 (1.38) | 4 | 2 | 0.389 | −1.488 |
| gltA | 389 | 10 | 0.397 | 12 (3.08) | 7 | 5 | 0.148 | −0.269 |
| aroE | 397 | 10 | 0.361 | 10 (2.52) | 5 | 5 | 0.377 | −0.913 |
| glk | 405 | 8 | 0.409 | 8 (1.98) | 6 | 2 | 0.173 | −0.613 |
| lepC | 420 | 8 | 0.392 | 8 (1.90) | 7 | 1 | 0.032 | 1.146 |
| Do scheme | ||||||||
| Locus | Fragment size (bp)c | No. of alleles | G + C Mol | No. polymorphic sites (%) | Synonymous changes | Non-synonymous changes | dN/dS | Tajima's D test |
| accC | 462 | 8 | 0.402 | 7 (1.52) | 5 | 2 | 0.146 | −1.637 |
| gki | 426 | 9 | 0.431 | 10 (2.35) | 8 | 2 | 0.044 | −1.079 |
| lepA | 441 | 7 | 0.414 | 8 (1.81) | 7 | 1 | 0.014 | −0.924 |
| recP | 474 | 13 | 0.403 | 11 (2.32) | 6 | 5 | 0.3 | −0.613 |
| sodA | 492 | 11 | 0.412 | 13 (2.64) | 6 | 7 | 0.152 | −1.767 |
| tyrS | 513 | 13 | 0.382 | 16 (3.12) | 12 | 4 | 0.063 | 0.404 |
| gtfB | 453 | 11 | 0.34 | 10 (2.21) | 2 | 8 | 0.536 | 0.351 |
| spaP | 513 | 8 | 0.395 | 13 (2.53) | 9 | 4 | 0.071 | −1.360 |
a
Number of S. mutans isolates used were Nakano scheme (n = 33) and Do scheme (n = 32). Data generated using DnaSP software v.5.10.1.
b
Fragment size reported in this study for Nakano scheme is slightly different than originally reported by Nakano et al. (2007).
c
Fragment size for Do scheme were trimmed to PubMLST length.