Data from: Whole genome-sequencing and phylogenetic analysis of a historical collection of Bacillus anthracis strains from Danish cattle

Derzelle S, Girault G, Kokotvic B, Angen Ø

Date Published: August 31, 2015

DOI: http://dx.doi.org/10.5061/dryad.0h82m

 

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Title S1 Fig. Evolutionary analyses of 52 strains of B. anthracis based on 29906 chromosomal SNPs.
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Description 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.
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Title Fig. 1 Position of the eleven Danish strains within the B. anthracis phylogenetic tree based on whole-genome SNP analysis.
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Description 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.
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When using this data, please cite the original publication:

Derzelle S, Girault G, Kokotvic B, Angen Ø (2015) Whole genome-sequencing and phylogenetic analysis of a historical collection of Bacillus anthracis strains from Danish cattle. PLoS ONE 10(8): e0134699. http://dx.doi.org/10.1371/journal.pone.0134699

Additionally, please cite the Dryad data package:

Derzelle S, Girault G, Kokotvic B, Angen Ø (2015) Data from: Whole genome-sequencing and phylogenetic analysis of a historical collection of Bacillus anthracis strains from Danish cattle. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.0h82m
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