MOESM6 of Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel

Additional file 6. WGS-SNP-based phylogenetic analysis of local M. bovis mastitis-associated isolates (n = 89) performed in comparison to a reference genome M. bovis PG45 as described in Materials and Methods. The phylogenetic tree was constructed by using the Maximum-Likelihood method, and bootstrapped 500 times to assess support for the different branches using MEGA-X [25]. The designation of the isolates includes serial number or sequencing identifier (for isolates sequenced in this study), name of the isolate, type of mastitis (clinical (CM) or subclinical (SM)) and year isolation. For additional information about particular strain, see Additional file 1: Table S1. Total SNP count resulted in 16,910 SNPs. Comparison between phylogenetic trees obtained by total-genome-based SNP analysis with (Additional file 6) and without (Fig. 3a) comparison to the reference genome revealed almost the same intergroup clustering of the isolates. However, the clade distribution of isolates was slightly different between these two comparisons. This file can be opened using MEGA software [25] or via public available servers, e.g. the NCBI Tree Viewer (https://www.ncbi.nlm.nih.gov/tools/treeviewer/), ETE Toolkit (http://etetoolkit.org/treeview/) etc.