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. 2020 May 4;117(20):11018–11028. doi: 10.1073/pnas.1917168117

Fig. 3.

Fig. 3.

The cattle specialist lineage genomes show evidence of host adaptation. (A) Gene presence/absence (black circles) and recombination regions (black bars) gained and lost on the tree branch differentiating ST-61 complex cattle specialist C. jejuni inferred using ClonalFrameML and mapped to the NCTC11168 reference genome. Accessory genes not mapped to NCTC11168 are also highlighted on the left (black circles, Upper). The relative abundance of genes was calculated as presence in ST-61 complex isolates minus presence in ST-21 complex isolates. The frequency of all genes/alleles (black circles/bars) is shown for ST-61 and ST-21 complexes (Upper and Lower). The homoplasic genes (red circles), including the glycosylation gene block, and recombinant alleles (red triangles) present or absent in ST-42 complex are shown (Upper and Lower). (B) Single-gene trees for nine candidate cattle-adaptive genes demonstrating homoplasy among cattle specialist lineages. Trees show intermingled clusters of isolates from the two cattle specialist lineages ST-61 (blue) and ST-42 (light blue), separated from the generalist lineage ST-21 (yellow).