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A genomic overview of the population structure of Salmonella

Fig 2

Correspondence between eBGs from legacy MLST and reBGs from rMLST.

The figure shows a GrapeTree clustering (MSTreeV2) [31] of 3,929 MLST STs from 118,391 Salmonella strains in EnteroBase. Each node corresponds to a single legacy ST, with diameter scaled to the number of strains. Strains whose ST assignments were based on legacy ABI sequencing are coloured black and strains whose ST assignments were based on genomic assemblies are indicated by unique colours for the 50 most prevalent reBGs. The colours, reBG designations, dominant serovar, and numbers of genomic assemblies are indicated in the key (top left). Lines connect nodes that are single-locus variants. The GrapeTree shows that most reBGs correspond to a single eBG cluster of single-locus variants of legacy STs (e.g., eBG1 corresponds to reBG1), but others correspond to subclusters (e.g., eBG14 includes reBG14.1, reBG14.2, and reBG14.3). This correspondence between eBG and reBG assignments was 1:1 for 243 eBGs/reBGs. In other consistent cases, 24 eBGs split into multiple related reBGs and 13 reBGs each encompass multiple related eBGs. An interactive version of the figure is available to registered EnteroBase users at http://enterobase.warwick.ac.uk/ms_tree?tree_id=9123. A full list of strains included is available on EnteroBase (https://enterobase.warwick.ac.uk/species/senterica/search_strains?query=workspace:9113).

Fig 2

doi: https://doi.org/10.1371/journal.pgen.1007261.g002