Additional File 5. Candidate LGT from prokaryotes to eukaryotes

Each tree is a Bayesian consensus tree, based on an alignment of homologues from one or more of the target taxa studied in this survey, where LGT from prokaryotes to eukaryotes is the most parsimonious explanation for the resulting tree topology. The key for the symbols used to differentiate the taxonomy of the analyses sequences and provide taxonomic contextualization for the candidate LGTs is indicated just after the list of trees. A parallel phylogenetic analyses was performed with pairwise maximum likelihood distances calculated with the same model used for the Bayesian analysis and bootstrap values estimated and mapped onto the Bayesian consensus tree. Only well-supported branches are indicated (posterior probabilities ≥ 0.95, bootstrap ≥ 0.7) on the trees with all other branches being collapsed into polytomies. The LGTs supported by at least one node (trees numbered ONXXX) or at least two nodes (trees numbered TNXXX) separating the target taxa from other eukaryotes are illustrated. Datasets where the target taxa are the only eukaryote (or with closely related taxa, the latter suggesting deep LGT prior speciation events) among prokaryotic sequences are also labeled as TNXXX. The accession number and annotations of the sequences from the target taxa (boxed in the trees) are indicated. A PHOBIUS analysis investigated the potential presence of a signal peptide (SP) and transmembrane domains (TMD).