Table 2. Shimodaira–Hasegawa (SH) analysis of gene phylogeny of individual sequences of 10 common type III effectors shared by all 25 citrus canker-causing Xanthomonas strains in comparison with the reference phylogeny based on core genome.
| Genea | −ln Lb | Diff −ln Lc | P-valued | Positive selectione |
|---|---|---|---|---|
| xopA_XAC0416 | 4 740 381 | 91 517.66 | 0.000* | Y |
| avrBs2_XAC0076 | 4 663 871 | 15 008.52 | 0.000* | N |
| xopE3_XAC3224 | 4 768 447 | 119 583.9 | 0.000* | N |
| hpaA_XAC0400 | 4 768 447 | 119 583.9 | 0.000* | Y |
| xopX_XAC0543 | 4 667 601 | 18 738.44 | 0.000* | Y |
| xopQ_XAC4333 | 4 768 447 | 119 583.9 | 0.000* | N |
| xopV_XAC0601 | 4 659 360 | 10 496.79 | 0.000* | Y |
| xopK_XAC3085 | 4 659 796 | 10 933.24 | 0.000* | N |
| xopAI_XAC3230 | 4 663 627 | 14 764.36 | 0.000* | N |
| xopE1_XAC0286 | 4 768 447 | 119 583.9 | 0.000* | N |
| Core genome | 4 648 863 | (Best) | – |
a
Gene name and corresponding gene loci in XacA306.
b
ln L, negative log-likelihood values correspond to those for the constrained topology.
c
Score differences between the unconstrained and constrained trees.
d
SH test. *P<0.05.
e
Under positive selection, ‘Y' denotes yes, ‘N' denotes no and ‘–' denotes not detected.