FIG 4.

Comparative genomics of mobile and core genomic chromosomal elements of venom-tolerant E. faecalis. (A) Circos coverage plots of the vancomycin resistance-associated V583 plasmids pTEF1, pTEF2, and pTEF3 in the E. faecalis isolates obtained from oral, envenomation 1 (E1), and envenomation 2 (E2) samples from three N. nigricollis individuals reinforce the two sequence type groupings and highlight within-animal variation (green arcs) indicative of sample-specific variation (lack of reads) across E2 samples in animals 1 and 2. The central plot for each plasmid and animal reflects GC content. All data are represented in 50-nt blocks. (B) Blind maximum likelihood tree of the core genomic alignments for the 6 N. nigricollis-derived E. faecalis isolates against the V583 and OG1RF reference strains, with color coding referring to the origin of the isolates: light blue, animal 1; dark blue, animal 2; yellow, animal 3. (C) Maximum likelihood tree from concatenated nucleotide sequence alignment of 865 core genes (381,319 bp) from 734 genomes after removing the sites with gaps. The best-fit GTR+I+G4 substitution model was used with 100,00 ultrafast bootstraps and SH-aLRT tests. The tree was rerooted on the longest branch, and branch lengths of <0.001 were collapsed. The scale bar shows number of nucleotide substitutions per site. Branches in red, blue, purple, and green show group A, group B, and clades containing strains V853 and OG1RF, respectively.