DOI: 10.5061/dryad.0h82m
title: Data from: Whole genome-sequencing and phylogenetic analysis of a historical collection of Bacillus anthracis strains from Danish cattle

description: Bacillus anthracis, the causative agent of anthrax, is known as one of the
 most genetically monomorphic species. Canonical single-nucleotide
 polymorphism (SNP) typing and whole-genome sequencing were used to
 investigate the molecular diversity of eleven B. anthracis strains
 isolated from cattle in Denmark between 1935 and 1988. Danish strains were
 assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4),
 A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and
 A.Br.Aust94 (n = 1). The match with the A.Br.Ames lineage is of particular
 interest as the occurrence of such lineage in Europe is demonstrated for
 the first time, filling an historical gap within the phylogeography of the
 lineage. Comparative genome analyses of these strains with 41 isolates
 from other parts of the world revealed that the two Danish A.Br.008/011
 strains were related to the heroin-associated strains responsible for
 outbreaks of injection anthrax in drug users in Europe. Eight novel
 diagnostic SNPs that specifically discriminate the different sub-groups of
 Danish strains were identified and developed into PCR-based genotyping
 assays.
description: S1 Fig. Evolutionary
 analyses of 52 strains of B. anthracis based on 29906 chromosomal
 SNPs.S1 Fig. Evolutionary
 analyses of 52 strains of B. anthracis based on 29906 chromosomal SNPs.
 Phylogenetic relationships were inferred using the Maximum Likelihood
 method (A), the Maximum Parsimony method (B), the Neighbor-Joining method
 (C) and the UPGMA method (D). Bootstrap values (100 iterations) higher
 than 70% are shown next to the branches. All evolutionary analyses were
 conducted in MEGA6 [28]. The maximum likelihood tree with the highest log
 likelihood (0.000) is shown in A. Tree #1 out of 2 most parsimonious trees
 (length = 7469, consistency index = 0.815, retention index = 0.947) is
 shown in B. The optimal neighbour-joining tree with the sum of branch
 length = 0.251 is shown in C. The optimal UPGMA tree with the sum of
 branch length = 0.239 is shown in D. The later tree is drawn to scale,
 with branch lengths in the same units as those of the evolutionary
 distances used to infer the phylogenetic tree.Figure
 S1.pptxFig. 1 Position of the
 eleven Danish strains within the B. anthracis phylogenetic tree based on
 whole-genome SNP analysis.Figure 1. Position of
 the eleven Danish strains from cattle within the B. anthracis phylogenetic
 tree based on whole-genome SNP analysis. Minimum spanning tree based on
 6596 chromosomal SNPs (A), 222 pXO1 SNPs (B) and 166 pXO2 SNPs (C). The 13
 different canSNP groups are color-coded: C.Br.A1055 in white, B.Br.CNEVA
 in yellow, B.Br.001/002 and B.Br.Kruger in orange, A.Br.011/009 in light
 blue, A.Br.008/011 in blue, A.Br.WNA in dark blue, A.Br.005/006 in pink,
 A.Br.003/004 in red, A.Br.001/002 in green, A.Br.WNA in dark green,
 A.Br.Aust94 in brown and A.Br.Vollum in purple. The position of the 11
 Danish isolates (in bold and underligned), the African IEMVT89 and 40
 available whole genome-sequenced strains is marked. The length of each
 branch is proportional (logarithmic scale) to the number of SNPs
 identified between strains. Indicated in red are the position and name of
 some new or published SNPs specific to various canSNP groups: A05
 (A.Br.005/006 group); A.Br.008 (A.Br.008/009 group); A08/D and A08/D1
 (A.Br.008/011); A.Br.011 (A.Br.011/009); A.Br.009 (A.Br.WNA); A.Br.002 and
 A01 (A.Br.001/002 and A.Br.Ames); A02, A02/A, A02/B, A02/B1 (A.Br.001/002
 subgroup A02); A.Br.001 and A01/A-DK (A.Br.Ames); A.Br.013, A.Br.015a,
 A.Br.15b, A.Br.026 (A.Br.Aust94). Based on a parsimony approach, the trees
 sizes are, respectively, 6730 (A), 227 (B) and 168 SNPs (C), i.e.
 containing approximately 1.9 (A), 2.2 (B) or 1.2 (C) % of homoplasia.The
 minimum spanning tree was drawn in BioNumerics version 6.6 (Applied Maths)
 using default settings.Figure 1 DK
 diversity.pptx