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. 2018 Feb 5;8:2393. doi: 10.1038/s41598-018-20889-x

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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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Accessory genome composition of the genomic clades of C. hyointestinalis. Clades are defined based on the congruence of the pangenome and phylogenetic analyses, as presented in Fig. 7. Gene groupings obtained by the use of get_homologues were used to define core and accessory genome components. Genes that are identified as unique to, and conserved within each defined clade are enumerated with respect to their functional category, as assigned using Eggnog-mapper⁷¹.