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Fig. 1 | BMC Genomics

Fig. 1

From: Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Fig. 1

Maximum likelihood pan-genome phylogeny of the genus Salmonella. The tree was estimated from the presence-absence matrix of 18,446 consensus homologous gene clusters found among 109 Salmonella spp. genomes with GET_HOMOLOGUES. Seventy-six of them correspond to a selection of S. enterica subsp. diarizonae sequences downloaded from ENTEROBASE, thirty-one to reference genomes from other species and serovars, and the remaining two to the Bolivian strains, SBO13 and SBO27. The matrix contains 4177 distinct patterns, 9276 parsimony-informative, 6963 singleton and 2207 constant sites. Nodal support values are color-coded as shown on the legend, the first value corresponding to approximate Bayesian support values and the second one to ultra-fast bootstrap values, as implemented in IQTREE. The scale represents the number of expected substitutions per site under the best-fitting GTR2 + F0 + R2 (binary) model. The phylogeny corresponds to the top-scoring tree (lnL = − 197,100.501) found among 10 independent IQTREE searches. It was rooted at the S. bongori clade. Labels for the 76 S. enterica subsp. diarizonae genomes fetched from ENTEROBASE indicate relevant ecological metadata and the sequence type (ST). Genomes in bold were selected for further analysis

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