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. 2018 Jul 12;8:10552. doi: 10.1038/s41598-018-28908-7

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Similarity in phylogeny generated from the chromosome and the accessory genome. (A) Phylogenetic relationship of plasmid genome as determined by Roary compared to a matrix with the presence (blue blocks) and absence (grey areas) of core and accessory genes found in the pangenome. Correlation between clades as determined by (B) SNP analysis of the chromosome and (C) pangenome analysis of the plasmid genome is illustrated. The relationship among the strains is consistent between the two methods although the absolute placement of the clade denoted as #3 differs.