Table 1.
Recombination and horizontal gene transfer (HGT) test results
|
Campylobacter 17 species, 495 core genes, 445 NR, 50 CR |
Clostridium 65 species, 120 core genes, 108 NR, 12 CR |
Legionella 47 species, 392 core genes, 348 NR, 44, CR |
Staphylococcus 36 species, 604 core genes, 556 NR, 48 CR |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus | PHI | SBP | HGT | PHI | SBP | HGT | PHI | SBP | HGT | PHI | SBP | HGT |
| rpoA | X | X | X | X | X | X | X | X | X | X | X | ✓ |
| rpoB | ✓ | ✓ | X | ✓ | X | X | X | X | X | X | X | X |
| rpoB* | X | X | X | X | X | X | X | X | ||||
| rpoC | ✓ | X | X | X | X | ✓ | X | X | X | ✓ | X | X |
| NR (%) | 0.38 | 0.15 | 0.32 | 0.11 | 0.03 | 0.41 | 0.01 | 0.02 | 0.08 | 0.09 | 0.07 | 0.22 |
| CR (%) | 0.12 | 0.08 | 0.16 | 0.08 | 0.00 | 0.08 | 0.05 | 0.02 | 0.23 | 0.02 | 0.00 | 0.79 |
| 16S | ✓ | ✓ | X | ✓ | X | ✓ | ✓ | ✓ | X | X | X | ✓ |
| 23S | X | X | X | X | X | ✓ | X | ✓ | X | X | X | ✓ |
| 5S | X | ✓ | X | ✓ | X | X | X | ✓ | ||||
| 16S M | ✓ | ✓ | X | X | ✓ | ✓ | X | X | ||||
| V1-2 | ✓ | X | X | X | X | X | X | |||||
| V3 | X | X | X | X | ||||||||
| V3 M | X | X | X | X | X | |||||||
| V3-V4 | X | X | X | X | X | X | X | X | ||||
| V3-V4 M | X | X | X | X | X | X | ||||||
| V4 | X | X | X | X | X | X | X | |||||
| V4 M | X | X | X | X | X | |||||||
| V5 | X | X | X | X | ||||||||
| V6 | X | X | X | X | ||||||||
| V7 | X | X | X | X | ||||||||
| V8 | X | X | X | X | ||||||||
| V9 | X | X | NP | NP | NP | X | ||||||
NR Non-ribosomal genes, CR Coding ribosomal genes, PHI Pairwise homoplasy index recombination analysis, SBP Single break-point recombination analysis, HGT HGTector analysis for protein coding genes and our phylogenetic approach to detect HGT for rRNA genes (see text), rpoB* partial rpoB sequence based on primers published by Ogier et al. [47], M masked locus, V hypervariable regions of the 16S rRNA gene, ✓ indicates loci positive for recombination or HGT, X indicates loci negative for recombination or HGT, blank cells indicate where metrics could not be obtained due to the nature of the locus (short gene length for PHI, not protein coding for HGTector, single-copy gene for phylogenetic HGT), NR and CR loci presented as proportion of genes positive for recombination or HGT, NP not possible (missing locus)