Describing ancient horizontal gene transfers at the nucleotide and gene level by comparative pathogenicity island genometrics

Supplementary data

François Collyn, Lionel Guy, Michael Marceau, Michel Simonet, Claude-Alain H. Roten, submitted.

All supplementary figures and tables are in pdf format

Supplementary Figure 1

NJ-ClustalW dendrogram of concatenated Pil amino acid sequences by . PAIs are depicted in bold type. The bar represents the evolutionary distance scale and the numbers on the branches indicate the number of times each particular topology was conserved in the 1000 trees generated by bootstrap analysis. PilN was not included in this analysis because it is truncated in SPI-7. We wish to emphasize that very similar trees were obtained when comparing individual genes (data not shown).

Supplementary Figure 2

Gene map comparisons of pil-harboring plasmids and PAIs: ortholog content (A) and gene order conservation (B): UPGMA (left) and NJ- dendrograms (right). PAIs are in bold type. Scale units and roots (if any) are defined as in Fig. 2. Dendrogram topologies were assessed using omit tests.

Supplementary Figure 3

Dinucleotide signature comparisons for the four PAIs: dendrograms of dinucleotide signature comparisons with orthologs (Fig. 1) located upstream (A), within (B) and downstream (C) of the pil operon and for the whole set of orthologs (D). From left to right: UPGMA, NJ- and Fitch Margoliash dendrograms. Scale units and roots (if any) are described in Fig. 3. Dendrogram topologies were assessed using omit tests.

Supplementary Figure 4

Dinucleotide signature comparison of PAIs and pil-encoding plasmids. Dendrograms of comparisons of pil operons (A) and whole plasmid sequences associated with PAI ortholog subsets without (B) or with pil genes (C). PAIs are in bold type. From left to right: UPGMA and Fitch Margoliash dendrograms. Clusters are conserved in all trees, except for the NJ representation in panel C. Scale units and roots (if any) are described in Fig. 3.

Supplementary Figure 5

Distance matrix of dinucleotide signature comparisons for SPI-7, YAPIs, 1 W14 and various plasmids. Distance units are described in Fig. 3.

Supplementary Figure 6

Bootstrapped NJ and Fitch Margoliash dendrograms of dinucleotide signature comparisons for SPI-7, YAPIs, 1 W14 and various Yersinia, Salmonella and Escherichia plasmids. The numbers on the branches indicate the number of times each particular topology was conserved in the 1000 trees generated by bootstrap analysis. Scale and distance units are described in Fig. 5.

Supplementary Table 1

Ortholog designation for YAPIpst, SPI-7ty, 1 W14 and YAPIent.

Supplementary Table 2

Chromosomal core genes used for amino acid identity comparison of Y. pseudotuberculosis and Y. enterocolitica.