Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

Girault G, Blouin Y, Vergnaud G, Derzelle S

Date Published: April 25, 2014

DOI: http://dx.doi.org/10.5061/dryad.rc6m9

 

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Title Figure 1: Phylogeny of 126 B. anthracis strains based on whole-genome SNP analysis
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Description Phylogeny of 126 B. anthracis strains based on whole-genome SNP analysis. A. Minimum spanning tree based on 3987 chromosomal SNPs (obtained with BioNumerics 6.6 from Applied Maths). The 3 canSNP groups present in France are color-coded: B.Br CNEVA in light blue, A.Br 011/009 in purple and A.Br 001/002 in green. The African lineage A.Br 005/006 is indicated in red. Positions of the B. anthracis Sterne (in green), Ames ancestor (in yellow) and A1055 (in black) strains are also marked. Each circle represents a unique SNP genotype. The diameter of each circle varies according to the number of isolates having the same genotype. 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 the new identified French canSNPs. The star marks the approximate branching point of the B. anthracis lineage within the B. cereus group. Based on a parsimony approach, the tree size is 4018, i.e. it contains approximately 0.77% of homoplasia. B. Linear phylogenetic tree rooted with the B. cereus AH820 strain as outgroup. This figure illustrates the relationship between French and globally diverse B. anthracis strains.
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Title Figure 2: Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage
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Description Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage (obtained with BioNumerics 6.6 from Applied Maths). Data are based on 345 chromosomal SNPs (A), 14 pXO1 SNPs (B) and 15 pXO2 SNPs (C). The geographic clustering of the French strains is color-coded: Alps in green (34 strains), Pyrenees in purple (9 strains), Massif Central in red (18 strains) and Saône et Loire department in yellow (6 strains). The diameter of each circle varies according to the number of isolates having the same genotype. 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 four French canSNPs described in this study. Based on a parsimony approach, the tree size is 352, i.e. it contains approximately 1.98% of homoplasia. Concerning the plasmids, the tree sizes are 14 and 15 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia.
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Title Figure 3: Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup
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Description Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup (obtained with BioNumerics 6.6 from Applied Maths). Data are based on 560 chromosomal SNPs (A), 20 pXO1 SNPs (B) and 18 pXO2 SNPs (C). The six resolved branches are color-coded. The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the positions and names for two canSNPs described in this study. NE: North-East, SW: South-West, SE: South-East. Based on a parsimony approach, the tree size is 561, i.e. it contains approximately 0.18% of homoplasia. Concerning the plasmids, the tree sizes are 20 and 18 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia.
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When using this data, please cite the original publication:

Girault G, Blouin Y, Vergnaud G, Derzelle S (2014) High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery. BMC Genomics 15: 288. http://dx.doi.org/10.1186/1471-2164-15-288

Additionally, please cite the Dryad data package:

Girault G, Blouin Y, Vergnaud G, Derzelle S (2014) Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.rc6m9
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