FIG 1.

(A) Phylogenetic tree of RF Borrelia species. Whole genomes were downloaded from GenBank (see Table S1 in the supplemental material for accession numbers) and aligned using progressiveMauve (40). Alignments of the eight housekeeping genes used in Borrelia multilocus sequence typing (uvrA, rplB, recG, pyrG, pepX, clpX, nifS, and clpA) (41) were extracted and concatenated, and a tree was created using maximum likelihood methodology and 500 bootstrap replicates in MEGA X (42). (B) Sequence alignment of the amplified region of Bh_0509 and homologs in other RF borreliae. The strains included are the same as those in panel A, except that B. hermsii YOR and B. miyamotoi FR64b are not included. Nucleotides that differ from the consensus are highlighted (red, A; yellow, G; blue, C; green, T). Arrows indicate primer and probe binding regions (5′ to 3′) and are annotated on the sequence to which they match exactly.