Fig. 4

Allelic diversity of the tfs3 ICE. a The ‘vir’ gene labelled tfs3 ICE gene cluster (top) is representative of the complete tfs3 ICE from strain Gambia94/24 (genes 7340–7535) used as reference for the ICE alignments and closely approximates the position of genes in the alignment schematic. Individual mVISTA graphs depict sequence similarity of tfs3 ICEs from strains P-41 (genes 0159–0204), A-5 (genes 1146–1181), PeCan18 (genes 4840–5050), UM114 (genes 1250–1445), CPY6311 (genes 0113–0153), India7 (genes 3720–3900), Shi112 (genes 1185–1415), Shi417 (genes 7490–7655), Aklavik117 (genes 2160–2315) and H. cetorum strain MIT 00–7128 (genes 8040–8260) relative to the Gambia94/24 tfs3 ICE in global pairwise sequence alignments using a 50 bp calculation window and 70% sequence identity cut-off. Labelled brackets indicate broad positional conservation of similar gene groupings as the tfs4 ICE. b Extent of sequence and gene content variability within the left flank of the tfs3 ICE. (Top) Schematic shows the complement of 20 genes in the left flank of the tfs3 ICE (virD2 [C9] to topA [C16] inclusive) annotated according to the nomenclature described in Table 1. Highly variable genes are block highlighted in orange. Relative position of genes closely approximates corresponding positions in the alignment graphs (bottom). Individual mVISTA graphs depict sequence similarity of tfs3 ICEs from 16 strains including strains P-41, H-29, SJM180, UM114, CPY6311, PeCan18, India7, OK310, Puno135, Shi112, Shi417, Aklavik117, H-3, P-13 and H. cetorum strain MIT 00–7128 relative to the Gambia94/24 tfs3 ICE (genes 7340–7425) using a 50 bp calculation window and 70% sequence identity cut-off. For both a. and b., the mid-line in individual alignment curves corresponds to 50% sequence identity to the Gambia94/24 reference tfs3 ICE sequence and regions with sequence identity ≥ 70% are indicated by blue (coding sequence) or red (non-coding intergenic sequence) shading. Gaps indicate absent genes