TABLE 5.
PERMANOVA analysis of core genome (SNP distance matrix), accessory genome (presence or absence of accessory genes), and virulence genes by region (n = 5) and farm (n = 18)
| Factor evaluated | Genomic data set | df | Pseudo-F | P value | Component of variation (%)a |
|---|---|---|---|---|---|
| Region | Core | 4 | 1.9 | 0.0975 | NS |
| Accessory | 4 | 2.69 | 0.0016 | 11.6 | |
| Virulence | 4 | 1.36 | 0.245 | NS | |
| Farm | Core | 17 | 28.6 | 0.0001 | 88.5 |
| Accessory | 17 | 9.3 | 0.0001 | 69.7 | |
| Virulence | 17 | 24.7 | 0.0001 | 86.8 |
a
Residual variation: core (11.5%), accessory (30.2%), and virulence (13.2%). NS, not significant.