Figure 2

A contig of Fusobacterium nucleatum shows a potential HGT event found by phylogenetic assignment and is supported by the compositional method. A) Five ORFs have been clearly detected (a sixth ORF could exist, but it has not been considered since the homology search results in partial, short matches). Four of these ORFs (shown in green) have been assigned to Fusobacterium taxa (Fusobacteriaceae). The best hit for the second ORF (shown in red) is a short protein found in Vibrio vulnificus (Gamma-proteobacteria), and no hits with Fusobacteriales have been found in that zone. This can be indicative of a putative foreign origin of that ORF. B) The zone also shows atypical composition, which is very apparent and easily seen in the compositional diagram. C) Clustering of the distance matrix of compositional correlations. A clustering parameter indicates the point at which the groups of compositionally similar ORFs are extracted. The lower the value, the fewer the transitions found, since rather dissimilar ORFs are allowed to fall into the same cluster. In this example, the DNA composition of ORF 2 is so different that it will be recognised as being atypical at all values of the clustering parameter.