Genetic relationships according to core SNPs, cgMLST and wgMLST.

<p>(A) Maximum parsimony genealogy of 73 genomes of serovar Agona based on 846 nonhomoplastic, nonrecombinant, nonmobile, nonrepetitive core SNPs. Modified from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007261#pgen.1007261.g001" target="_blank">Fig 1</a> of Zhou et al. [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007261#pgen.1007261.ref020" target="_blank">20</a>]. Groups A and D (key) refer to the subgroups labelled A2 and A1, and D1 and D2, respectively, in that figure. An interactive version of this phylogram is available to EnteroBase users (<a href="http://enterobase.warwick.ac.uk/phylo_tree?tree_id=10290" target="_blank">http://enterobase.warwick.ac.uk/phylo_tree?tree_id=10290</a>). (B) GrapeTree [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007261#pgen.1007261.ref031" target="_blank">31</a>] of cgMLST (3,002 loci) from 1,082 Agona genomes in EnteroBase, consisting of all Agona genomes assembled by EnteroBase from the ENA short-read archives, including the genomes in part A plus additional genomes from the Irish 2008 outbreak. An interactive version of this tree is available at <a href="http://enterobase.warwick.ac.uk/ms_tree?tree_id=9946" target="_blank">http://enterobase.warwick.ac.uk/ms_tree?tree_id=9946</a>. The entire set of genomes and all its metadata and genotyping results are available to registered EnteroBase users at <a href="http://enterobase.warwick.ac.uk/species/senterica/search_strains?query=workspace:12810" target="_blank">http://enterobase.warwick.ac.uk/species/senterica/search_strains?query=workspace:12810</a>. Scale bar for 5 loci at right. (C) GrapeTree of wgMLST (21,065 loci) of the same genomes as in part B. Scale bar for 30 loci at the right. An interactive version of this tree is available at <a href="http://enterobase.warwick.ac.uk/ms_tree?tree_id=9947" target="_blank">http://enterobase.warwick.ac.uk/ms_tree?tree_id=9947</a>. Parts B and C are colour coded by country of isolation. Additional metadata such as year of isolation or source of isolation can be investigated in the interactive versions.