Additional file 4: Figure S1. of Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia

Core genome phylogenies of Group I strains. A) Core genome phylogeny of C. botulinum Group I strains inferred with RAxML [63] using the ASC_GTRGAMMA model on an alignment of 182,200 core genome SNPs produced with NASP [61] using C. sporogenes ATCC 15579 [GenBank:ABKW00000000] as the reference genome. The consistency index is 0.56, and the retention index is 0.91 (computed with the R package phangorn). B) Core genome phylogeny of Group I strains inferred with FastTree2 [54] on a 1780-character core SNP matrix generated with kSNP [59]. The consistency index is 0.64, and the retention index is 0.93. The phylogenies were rooted with the clade that includes C. sporogenes and C. botulinum bont/B serotypes (bottom of Figure). Gray circles indicate bootstrap values over 95 %. While there are small variations in the phylogenies generated with different methods (Fig. 5 and Additional file 4: Figure S1), the overall topology of the Group I tree appears robust. The pairwise overall topological scores computed by Compare2Trees [69] range from 80 to 86 % for the phylogenies presented in Fig. 5 and (Additional file 4: Figure S1). (PDF 59 kb)