Predicted LGT-derived genes from Bacteria, Archaea and viruses encoded in the genomes of free-living and parasitic amoebae. LGT-derived genes were predicted using a phylogenomics approach consisting of an initial similarity-based screening using SIMAP , several filtering steps to extract amoebal proteins with prokaryotic best hits, followed by automatic calculation and manual inspection of phylogenetic trees using PhyloGenie and PHAT . (a) Percentage of lineage-specific LGT candidates in each genome; the absolute number of LGT candidates per genome is indicated next to each bar. (b) Heat map illustrating the Bray-Curtis similarity of the taxonomic affiliation (at the level of classes within the domain Bacteria) of putative LGT donors. (c) Ecological classification of putative LGT donors with respect to their oxygen requirement and association with a host. The ecology of putative donors was extrapolated from the lifestyles of the respective closest extant relatives.
Clarke et al. Genome Biology 2013 14:R11 doi:10.1186/gb-2013-14-2-r11