Table 1. Data and phylogenetic analysis of essential genes encoded on plasmids.
Essential list indicates the source of essential genes: TKP is TraDIS-Keio-PEC, TP is TraDIS-PEC, T is TraDIS (Goodall et al. 2018); LB, M9 and GMM means this gene is essential in each of the three medias (Rousset et al. 2020). Relaxed selection shows evidence for relaxed selection on plasmid homologs’ branch was found using HyPhy-RELAX (Murrell et al. 2012). Tree topology shows the conclusions from the phylogenetic reconstruction of essential genes on plasmids and chromosomes: split between plasmids and chromosomes describe phylogenies that had a deep split between plasmid and chromosomal homologs (i.e., they are diverged); LGT events from chromosome to plasmid are labeled by transfer to plasmid; LGT events from plasmid to chromosome are labeled by transfer to chromosome; mixed is used to label phylogenies that contain deep divergence and LGT events. For gene trees with evidence for gene transfer (groEL, groES), we further tested the support in the plasmid/chromosome split while excluding the putatively transferred gene. In all tested cases the result showed that the constrained tree could not be rejected in a topology test, thus validating the gene transfer inference. All of the transfer event from plasmid to chromosome are better described as translocation of the plasmid homolog to chromosome.
| Gene | Product | Essential list | No. Plasmids | No. Isolates | Relaxed selection | Tree topology |
|---|---|---|---|---|---|---|
| ssb | single-stranded DNA-binding protein | TKP | 420 | 320 | n.a. | Mixed |
| groL | chaperonin GroEL | TP | 11 | 11 | On plasmid branch | One translocation to Chromosome |
| groS | co-chaperone GroES | TKP | 13 | 13 | No evidence | One translocation to Chromosome |
| dnaB | replicative DNA helicase | TKP | 31 | 31 | No evidence | Two translocations to Chromosome |
| ubiX | aromatic acid decarboxylase | T | 1 | 1 | n.a. | Split between plasmids and chromosomes |
| nrdB | ribonucleotide-diphosphate reductase subunit beta | TKP | 20 | 20 | No evidence | Split between plasmids and chromosomes |
| nrdA | ribonucleoside-diphosphate reductase subunit alpha | TKP | 19 | 19 | On plasmid branch | Split between plasmids and chromosomes |
| ftsH | ATP-dependent metalloprotease FtsH | TKP | 2 | 2 | n.a. | Three transfers to plasmid |
| def | peptide deformylase | TKP | 13 | 13 | No evidence | Split between plasmids and chromosomes |
| dnaC | DNA replication protein DnaC | TKP | 1 | 1 | n.a. | Single transfer to plasmid |
| metG | methionine—tRNA ligase | TKP | 19 | 19 | No evidence | Mixed |
| ilvC | ketol-acid reductoisomerase, NAD(P)-binding | M9 | 3 | 3 | No evidence | Split between plasmids and chromosomes |
| glnS | glutamine—tRNA ligase | TKP | 5 | 5 | n.a. | Five transfers to plasmid |
| lolC | lipoprotein-releasing ABC transporter permease subunit | TKP | 2 | 2 | n.a. | Split between plasmids and chromosomes |
| proB | gamma-glutamate kinase | M9 | 2 | 2 | n.a. | Two transfers to plasmid |
| proA | gamma-glutamylphosphate reductase | M9 | 2 | 2 | n.a. | Two transfers to plasmid |
| kdsD | D-arabinose 5-phosphate isomerase | LB, GMM | 1 | 1 | n.a. | Split between plasmids and chromosomes |