TABLE 3.
Descriptive analysis of nucleotide sequence data
| Species (n) and gene | Length in bp (% of full ORF) | No. of variable sites | No. of mutations | No. of alleles | GC content | π/siteb | kc | Tajima's Dd | No. of mutations |
dN/dSe | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Synonymous | Nonsynonymous | ||||||||||
| All sequences (66)a | |||||||||||
| addB | 669 (20.1) | 283 | 418 | 43 | 35.10 | 0.1715 | 114.75 | NA | NA | NA | 0.08 |
| ldh | 711 (75.4) | 201 | 277 | 48 | 42.20 | 0.0970 | 68.95 | NA | NA | NA | 0.01 |
| lmo0490 | 611 (69.7) | 155 | 203 | 50 | 39.50 | 0.0810 | 49.50 | NA | NA | NA | 0.02 |
| prs | 511 (53.4) | 143 | 180 | 36 | 41.40 | 0.0808 | 46.48 | NA | NA | NA | 0.02 |
| polC | 695 (16.0) | 222 | 329 | 41 | 36.90 | 0.1312 | 90.43 | NA | NA | NA | 0.02 |
| pbpA | 871 (35.1) | 223 | 330 | 41 | 37.40 | 0.1254 | 91.32 | NA | NA | NA | 0.04 |
| LMO2763 | 958 (70.8) | 232 | 297 | 48 | 39.60 | 0.0779 | 74.40 | NA | NA | NA | 0.02 |
| lmo1555 | 495 (68.6) | 282 | 442 | 39 | 33.60 | 0.2457 | 116.15 | NA | NA | NA | 0.21 |
| rarA | 574 (44.7) | 188 | 277 | 39 | 39.60 | 0.1276 | 71.82 | NA | NA | NA | 0.03 |
| sigB | 660 (84.6) | 161 | 218 | 48 | 38.20 | 0.0866 | 57.07 | NA | NA | NA | 0.01 |
| L. monocytogenes (29) | |||||||||||
| addB | 669 (20.1) | 115 | 112 | 18 | 36.30 | 0.0716 | 47.91 | 2.09* | 97 | 18 | 0.07 |
| ldh | 711 (75.4) | 91 | 97 | 19 | 41.60 | 0.0447 | 31.77 | 1.10 | 92 | 5 | 0.01 |
| lmo0490 | 611 (69.7) | 66 | 71 | 21 | 39.80 | 0.0303 | 18.53 | 0.10 | 66 | 5 | 0.01 |
| prs | 511 (53.4) | 42 | 42 | 12 | 41.40 | 0.0240 | 13.26 | 0.89 | 42 | 0 | NA |
| polC | 695 (16.0) | 92 | 99 | 13 | 36.90 | 0.0523 | 36.25 | 1.63 | 98 | 1 | 0.00 |
| pbpA | 871 (35.1) | 115 | 130 | 13 | 38.40 | 0.0530 | 46.08 | 1.51 | 113 | 12 | 0.03 |
| LMO2763 | 958 (70.8) | 96 | 108 | 19 | 40.40 | 0.0286 | 27.28 | −0.03 | 106 | 2 | 0.00 |
| lmo1555 | 495 (68.6) | 135 | 154 | 16 | 33.90 | 0.1143 | 56.12 | 1.67 | 72 | 55 | 0.22 |
| rarA | 574 (44.7) | 51 | 56 | 13 | 40.60 | 0.0298 | 16.79 | 0.67 | 50 | 4 | 0.01 |
| sigB | 660 (84.6) | 74 | 80 | 17 | 38.80 | 0.0355 | 23.40 | 0.57 | 74 | 3 | 0.02 |
| L. innocua (12) | |||||||||||
| addB | 669 | 30 | 30 | 9 | 34.00 | 0.0120 | 8.02 | −0.87 | 37 | 2 | 0.02 |
| ldh | 711 | 55 | 57 | 10 | 43.60 | 0.0291 | 20.71 | 0.45 | 26 | 4 | 0.03 |
| lmo490 | 611 | 45 | 46 | 9 | 39.80 | 0.0214 | 13.09 | −0.64 | 54 | 3 | 0.02 |
| prs | 511 | 28 | 28 | 9 | 42.70 | 0.0126 | 6.95 | −1.12 | 45 | 1 | 0.00 |
| polC | 695 | 39 | 41 | 10 | 38.00 | 0.0150 | 10.39 | −1.07 | 28 | 0 | NA |
| pbpA | 871 | 40 | 40 | 10 | 37.20 | 0.0141 | 12.26 | −0.34 | 36 | 5 | 0.03 |
| lmo2763 | 958 | 39 | 39 | 9 | 39.30 | 0.0137 | 13.15 | 0.08 | 38 | 2 | 0.01 |
| lmo1555 | 495 | 30 | 30 | 6 | 32.80 | 0.0150 | 7.45 | −1.12 | 38 | 0 | NA |
| rarA | 574 | 36 | 38 | 9 | 38.70 | 0.0221 | 12.68 | 0.04 | 17 | 13 | 0.21 |
| sigB | 660 | 21 | 22 | 10 | 37.20 | 0.0128 | 8.42 | 0.69 | 19 | 3 | 0.05 |
| L. marthii (3) | |||||||||||
| addB | 669 | 1 | 1 | 2 | 36.00 | 0.0010 | 0.66 | NA | 0 | 1 | NA |
| ldh | 711 | 20 | 20 | 3 | 43.70 | 0.0188 | 13.33 | NA | 19 | 1 | 0.02 |
| lmo490 | 611 | 24 | 24 | 3 | 41.20 | 0.0262 | 16.00 | NA | 21 | 3 | 0.04 |
| prs | 633 | 9 | 9 | 3 | 42.90 | 0.0109 | 6.00 | NA | 9 | 0 | NA |
| polC | 695 | 28 | 28 | 3 | 39.20 | 0.0268 | 18.67 | NA | 28 | 0 | NA |
| pbpA | 871 | 8 | 8 | 3 | 38.30 | 0.0061 | 5.33 | NA | 8 | 0 | NA |
| lmo2763 | 958 | 13 | 13 | 3 | 40.30 | 0.0091 | 8.67 | NA | 13 | 0 | NA |
| lm01555 | 495 | 4 | 4 | 3 | 33.50 | 0.0054 | 2.67 | NA | 2 | 2 | 0.26 |
| rarA | 574 | 7 | 7 | 3 | 40.20 | 0.0081 | 4.67 | NA | 5 | 2 | 0.12 |
| sigB | 660 | 10 | 10 | 3 | 37.30 | 0.0101 | 6.67 | NA | 10 | 0 | NA |
| L. welshimeri (7) | |||||||||||
| addB | 669 | 4 | 4 | 4 | 33.50 | 0.0017 | 1.14 | −1.43 | 2 | 2 | 0.27 |
| ldh | 711 | 12 | 12 | 5 | 42.40 | 0.0071 | 5.05 | 0.17 | 12 | 0 | NA |
| lmo490 | 611 | 10 | 10 | 7 | 37.20 | 0.0053 | 3.24 | −1.11 | 10 | 0 | NA |
| prs | 511 | 4 | 4 | 4 | 40.00 | 0.0024 | 1.33 | −0.88 | 4 | 0 | NA |
| polC | 695 | 11 | 11 | 6 | 36.40 | 0.0069 | 4.76 | 0.33 | 10 | 1 | 0.02 |
| pbpA | 871 | 11 | 11 | 7 | 38.10 | 0.0058 | 4.67 | 0.21 | 8 | 3 | 0.12 |
| lmo2763 | 958 | 16 | 16 | 7 | 39.40 | 0.0056 | 5.33 | −1.02 | 15 | 1 | 0.02 |
| lmo1555 | 495 | 7 | 7 | 6 | 30.90 | 0.0048 | 2.38 | −0.86 | 3 | 4 | 0.48 |
| rarA | 574 | 8 | 8 | 7 | 39.20 | 0.0060 | 3.43 | 0.26 | 7 | 1 | 0.03 |
| sigB | 660 | 8 | 8 | 7 | 36.90 | 0.0040 | 2.67 | −0.96 | 6 | 2 | 0.08 |
| L. seeligeri (7) | |||||||||||
| addB | 669 | 22 | 22 | 7 | 33.70 | 0.0110 | 7.33 | −1.03 | 15 | 7 | 0.16 |
| ldh | 711 | 17 | 19 | 7 | 42.00 | 0.0118 | 8.38 | 0.45 | 19 | 0 | NA |
| lmo490 | 611 | 68 | 74 | 7 | 38.60 | 0.0481 | 29.38 | −0.16 | 69 | 5 | 0.02 |
| prs | 553 | 13 | 15 | 5 | 42.20 | 0.0084 | 4.67 | −1.31 | 15 | 0 | NA |
| polC | 695 | 30 | 32 | 7 | 37.60 | 0.0143 | 9.90 | −1.38 | 30 | 2 | 0.02 |
| pbpA | 871 | 31 | 31 | 6 | 38.10 | 0.0108 | 9.43 | −1.46 | 30 | 1 | 0.01 |
| lmo2763 | 958 | 31 | 31 | 7 | 37.70 | 0.0121 | 11.62 | −0.47 | 31 | 0 | NA |
| lmo1555 | 495 | 32 | 32 | 5 | 33.20 | 0.0204 | 10.10 | −1.30 | 22 | 10 | 0.14 |
| rarA | 574 | 43 | 45 | 5 | 38.90 | 0.0226 | 12.95 | −1.70* | 37 | 8 | 0.07 |
| sigB | 660 | 30 | 31 | 7 | 38.60 | 0.0174 | 11.48 | −0.53 | 29 | 2 | 0.02 |
| L. ivanovii (8) | |||||||||||
| addB | 669 | 33 | 33 | 3 | 36.10 | 0.0258 | 17.29 | 1.90† | 27 | 6 | 0.07 |
| ldh | 711 | 33 | 33 | 4 | 40.70 | 0.0241 | 17.11 | 1.83† | 31 | 2 | 0.01 |
| lmo490 | 611 | 46 | 46 | 3 | 38.90 | 0.0394 | 24.07 | 1.92† | 41 | 5 | 0.03 |
| prs | 553 | 30 | 30 | 3 | 40.90 | 0.0287 | 15.86 | 1.96† | 30 | 0 | NA |
| polC | 695 | 26 | 26 | 2 | 37.00 | 0.0200 | 13.93 | 2.05* | 23 | 3 | 0.04 |
| pbpA | 871 | 38 | 38 | 2 | 37.20 | 0.0234 | 20.36 | 2.08* | 35 | 3 | 0.02 |
| lmo2763 | 958 | 67 | 67 | 3 | 38.80 | 0.0372 | 35.61 | 2.05* | 63 | 4 | 0.02 |
| lmo1555 | 495 | 21 | 21 | 3 | 35.10 | 0.0219 | 10.86 | 1.78† | 10 | 11 | 0.31 |
| rarA | 574 | 22 | 22 | 2 | 38.50 | 0.0205 | 11.79 | 2.04* | 16 | 6 | 0.11 |
| sigB | 660 | 25 | 25 | 4 | 39.50 | 0.0197 | 13.00 | 1.83† | 23 | 2 | 0.02 |
a
These sequences were obtained from 50 isolates as well as 16 publicly available genomes (see Table 1 for more information).
b
Average number of pair-wise nucleotide differences per site.
c
Average number of pair-wise nucleotide differences per sequence.
d
Tajima's D was not inferred for (i) all isolates (because it is a population genetics statistic) or for (ii) L. marthii (because of the small number of isolates), and such cases are marked as not available (NA). *; P < 0.05; †, 0.05 < P < 0.10.
e
If the number of synonymous or nonsynonymous mutations could not be unambigiously inferred, the result is reported as not available (NA).