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Fig. 3 | BMC Genomics

Fig. 3

From: Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

Fig. 3

Maximum likelihood phylogenomic tree of Salmonella enterica subsp. enterica serovars (n = 440) from potential mono- and multi-animal sources. Based on pseudogenomes inferred with the variant calling workflow iVARCall2, the workflow IQ-Tree selected the most appropriate model of evolution (GTR + I + G4) according to Akaike Information Criteria (AIC) and reconstructed the tree with an ultrafast approximation of phylogenomic bootstrap. The present phylogenomic tree was inferred including SNPs from recombination events and was rooted using the most closely related indica subspecies as an outgroup. The potential mono- and multi-animal sources were assigned based on Chi-square tests of uniformity applied on a curated and synthetic subset of Enterobase. Examples of mutations associated with animal sources by microbial GWAS are presented (i.e. Wald tests). These associated mutations refer to polygenicity with regard to Quantile-Quantile (QQ) plots from microbial GWAS (i.e. p < 1 × 10− 2) and present high (i.e. > 5%) and low (i.e. < 5‰) frequencies of presence (i.e. genes and alternative variants) in the studied and compared genomes, respectively. The serovars (i.e. colored squares), potential sources (i.e. black and grew squares), animal sources (i.e. colored squares), as well as annotated (i.e. colored circles) and non-annotated (i.e. colored triangles) mutations associated to animal sources, are represented from the internal to external rings. The colored circles and triangles represent present genes or alternative variants, whereas missing data refers to absente genes or reference variants, respectively. Most of the branches of the tree (i.e. 85%) are supported by bootstrap values higher than 90% (i.e. black circles) and the corresponding newick file is accessible under request

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