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.