Fig. 1

Sources of genomic contamination. Three types of issues lead to contamination of genomic sequence data: biological, experimental and computational. The contamination of “pure” cultures can be due to both experimental (e.g. accidental introduction of contaminating microorganisms) and biological causes (e.g. the presence of an endosymbiont). Redundant contamination occurs when a genomic segment is present multiple times in a genome (e.g. multiple SSU rRNAs from different organisms). Non-redundant contamination occurs when a genomic region of the main organism, the expected one, is replaced by the corresponding region of a foreign organism (e.g. the SSU rRNA of the main organism is replaced by the SSU rRNA from a foreign organism). An extra DNA segment, not part of the main organism but belonging to a contaminant, would also be considered as a non-redundant contamination (e.g. eukaryotic DNA in a bacterial genome). A mixed scenario is also possible, as represented in the redundant contamination part of the figure