TABLE 2.
Sequence variation statistics and diversity parameters among 37 Clavibacter michiganensis subsp. michiganensis strains isolated in Iran calculated using DnaSP 5.10
| Province | Gene | No. of: |
Haplotype frequencya | Total no. of segregating sites | % polymorphic sites | Nucleotide diversity (π) | No. of mutations (η) | Haplotype (gene) diversity | Value for indicated neutrality testb |
Minimum no. of recombination events | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Strains | Nucleotides | Haplotypes | Tajima’s D | Fu and Li’s D* | Fu and Li’s F* | |||||||||
| East Azerbaijan | atpD | 10 | 455 | 3 | 0.300 | 4 | 0.879 | 0.308 × 10−2 | 4 | 0.600 | −0.037 NS | −0.338 NS | −0.296 NS | 0 |
| gyrB | 10 | 468 | 2 | 0.200 | 1 | 0.213 | 0.114 × 10−2 | 1 | 0.533 | 1.302 NS | 0.804 NS | 1.026 NS | 0 | |
| ppk | 10 | 495 | 3 | 0.300 | 16 | 3.232 | 0.154 × 10−1 | 16 | 0.644 | 1.627 NS | 0.799 NS | 1.132 NS | 0 | |
| recA | 10 | 415 | 3 | 0.300 | 3 | 0.722 | 0.225 × 10−2 | 3 | 0.644 | −0.431 NS | −0.804 NS | −0.798 NS | 0 | |
| rpoB | 10 | 277 | 1 | 0.100 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | |
| Concatenated | 10 | 2,110 | 5 | 0.500 | 24 | 1.137 | 0.498 × 10−2 | 24 | 0.800 | 1.135 NS | 0.405 NS | 0.662 NS | 1 | |
| Qazvin | atpD | 6 | 455 | 3 | 0.500 | 4 | 0.879 | 0.410 × 10−2 | 4 | 0.733 | 0.355 NS | 0.071 NS | 0.139 NS | 0 |
| gyrB | 6 | 468 | 3 | 0.500 | 5 | 1.068 | 0.484 × 10−2 | 5 | 0.600 | 0.196 NS | 0.362 NS | 0.348 NS | 0 | |
| ppk | 6 | 495 | 3 | 0.500 | 14 | 2.828 | 0.943 × 10−2 | 14 | 0.600 | −1.466 NS | −1.504*, P < 0.05 | −1.623 NS | 0 | |
| recA | 6 | 415 | 1 | 0.166 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | |
| rpoB | 6 | 277 | 1 | 0.166 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | |
| Concatenated | 6 | 2,110 | 5 | 0.833 | 23 | 1.090 | 0.417 × 10−2 | 23 | 0.933 | −0.793 NS | −0.834 NS | −0.900 NS | 1 | |
| West Azerbaijan | atpD | 8 | 455 | 3 | 0.375 | 2 | 0.439 | 0.212 × 10−2 | 2 | 0.607 | 0.931 NS | 1.111 NS | 1.167 NS | 0 |
| gyrB | 8 | 468 | 1 | 0.125 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | |
| ppk | 8 | 495 | 2 | 0.250 | 10 | 2.020 | 0.505 × 10−2 | 10 | 0.250 | −1.741*, P < 0.05 | −1.906*, P < 0.05 | 2.069*, P < 0.05 | 0 | |
| recA | 8 | 415 | 2 | 0.250 | 3 | 0.722 | 0.181 × 10−2 | 3 | 0.250 | −1.447 NS | −1.565 NS | −1.685 NS | 0 | |
| rpoB | 8 | 277 | 1 | 0.125 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | |
| Concatenated | 8 | 2,110 | 3 | 0.375 | 15 | 0.710 | 0.200 × 10−2 | 15 | 0.607 | −1.389 NS | −1.504 NS | −1.641 NS | 0 | |
| Zanjan | atpD | 8 | 455 | 4 | 0.500 | 5 | 0.098 | 0.502 × 10−2 | 5 | 0.821 | 0.840 NS | 0.747 NS | 0.846 NS | 0 |
| gyrB | 8 | 468 | 1 | 0.125 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | |
| ppk | 8 | 495 | 2 | 0.250 | 1 | 0.202 | 0.051 × 10−2 | 1 | 0.250 | −1.054 NS | −1.126 NS | −1.203 NS | 0 | |
| recA | 8 | 415 | 1 | 0.125 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | |
| rpoB | 8 | 277 | 1 | 0 | 0.000 | 0.000 | 0 | 0.000 | ND | ND | ND | ND | ||
| Concatenated | 8 | 2,110 | 6 | 0.750 | 9 | 0.426 | 0.156 × 10−2 | 9 | 0.929 | −0.261 NS | −0.386 NS | −0.396 NS | 0 | |
a
Number of haplotypes/number of strains.
b
ND, not determined; NS, not significant. Asterisks with data, P ≤ 0.05.