plosone-phylo
pone.0038969.g002.png
RaxML phylogeny based on the SNPs obtained after the alignment of the core genome.A. In this analysis, the strain N315 was included and used as outgroup. B. Same analysis as in A with bootstrap values given for each node. Nodes that were under the 50% majority rule were collapsed. The tree was rooted with N315 but the distance between this strain and the other was shortened to focus on the relationships between the eight isolates. C. Phylogeny based on the SNPs of the core genome based on the comparison of the eight isolates. D. Mapping of the MGEs and major differences observed between the different isolates onto the phylogenetic tree. Plasmids are represented by circle. The light blue and green circles represent the plasmids that are closely related to the published plasmid SAP064A and pUSA03, respectively. The black trait at the left side of the plasmids represents the presence of the mercuric operon whereas those on the right represent insertions of IS elements. The purple square illustrates the presence of an element of phage of about 18’500 bp. The smaller symbols describe the genetic variations described in Table 2. Circles were used for deletions, triangles for insertions and squares for other types of modifications. The numbers within each symbol correspond to the genetic variation described in Table 2. The symbols are white when the difference is unique to one isolate and colored when it is shared between different isolates.
pone.0038969.g002.png
RaxML phylogeny based on the SNPs obtained after the alignment of the core genome.A. In this analysis, the strain N315 was included and used as outgroup. B. Same analysis as in A with bootstrap values given for each node. Nodes that were under the 50% majority rule were collapsed. The tree was rooted with N315 but the distance between this strain and the other was shortened to focus on the relationships between the eight isolates. C. Phylogeny based on the SNPs of the core genome based on the comparison of the eight isolates. D. Mapping of the MGEs and major differences observed between the different isolates onto the phylogenetic tree. Plasmids are represented by circle. The light blue and green circles represent the plasmids that are closely related to the published plasmid SAP064A and pUSA03, respectively. The black trait at the left side of the plasmids represents the presence of the mercuric operon whereas those on the right represent insertions of IS elements. The purple square illustrates the presence of an element of phage of about 18’500 bp. The smaller symbols describe the genetic variations described in Table 2. Circles were used for deletions, triangles for insertions and squares for other types of modifications. The numbers within each symbol correspond to the genetic variation described in Table 2. The symbols are white when the difference is unique to one isolate and colored when it is shared between different isolates.