Table 1.
Comparison of the sequence types of B. afzelii strains according to multi locus sequence typing (MLST), and ospA and ospC typing.
Table 2.
Comparison of the replicons found in Borrelia afzelii K78 to the published sequences of B. afzelii strains ACA-1, PKo and B. burgdorferi strain B31.
Table 3.
Comparison of the K78 chromosome to representative chromosomes within Borrelia.
Fig 1.
Chromosomal region of 5S-23S rRNA and 16S rRNA for the B. afzelii strains K78, ACA-1, PKo, Tom3107, HLJ01 and for B. burgdorferi B31.
The rRNAs (marked red), are presented with transcription from right to left as located on the chromosome, and are composed of two copies of 16S rRNA, separated by tRNA-Ala. A tRNA-Ile (transcribed left to right) precedes the tandem repeats of the 23S-5S cassette. In many cases one of the 16S copies has undergone degeneration. In the case of ACA-1 the two contigs constituting the chromosome are separated at the position where the second 23S rRNA copy is expected (vertical red line), meaning the presence or absence of the second copy of 23S rRNA could not be determined due to the lower sequencing quality in this region. There is a high sequence homology among the four B. afzelii strains (except for the second copy of 23S rRNA of ACA-1) in contrast to the sequences in B. burgdorferi B31 rRNAs. The similarity score plots of the Mauve alignments use the backbone color scheme [43] which shows overall similarity in a mauve color or clustering blocks among cluster members in the same color.
Table 4.
Functional classification of the B. afzelii K78 annotated genome, describing a total of 1,309 proteins.
Table 5.
Number of predicted membrane proteins in four B. afzelii strains and B. burgdorferi B31.
Fig 2.
Alignment of B. afzelii K78 ospC sequence against the sequences of B. afzelii strains from public databases.
A non-redundant set of partial ospC sequences according to BAFK78_B0019 bp 97–583, comprising 59 B. afzelii strains and the sequence of B. burgdorferi B31 as external root reference were included in the analyses. A: Maximum likelihood tree representation, re-rooted with B. burgdorferi B31 as outgroup. Clusters containing strains attributed to human infectivity are boxed, of which the previously identified groups were labelled A1–A8. The strains compared in this study are highlighted in blue. B: A recombination network representation is shown for the sequences in an unrooted distance phylogram. The pairwise homoplasy index test for the B. afzelii sequences (p = 7.8x10-15) indicates significance for the presence of recombination events. The strains compared in this study are highlighted by a yellow background.
Fig 3.
Telomere types of the linear replicons.
Alignment of the telomeres of the linear replicons in B. afzelii K78 is shown. The sequences are oriented such that their hairpin bend would be positioned to their left side. The typing corresponds to the classification of the telomere types 1–3 according to the spacing between Box 1 (yellow) and Box 3 (blue) or the absence of Box 1 [68, 99, 101]. For five of the sequences the utmost left residue could not be determined and is represented by a “-”as placeholder. Box 1 and Box 3 correspond to previously annotated regions of conservation which are assumed to be directly (Box 3) or indirectly (Box 1) involved in interaction with the telomere resolvase ResT [100, 102]. No telomere data could be obtained for K78 lp28 and the telomeres of lp54L and lp38R are identical. In Box 1 two different sequences, TAT(A/T)AT, are present as in B31. Unlike in B31, where the TATTAT sequence is exclusively found in type 2 telomeres, this sequence is also found in type 1 telomeres of K78. lp28–1L of K78 is an exception while it is compatible with both the definition of type 1 and type 2 telomeres as also seen on lp28–3R of B31 and lp28–2R of PKo. Within the 16 telomeres, 6 have substitutions in Box 3 (5 with one change, and 1 with two changes, marked green).
Fig 4.
Species-specific variation of the intergenic variable region in the circular plasmid cp26.
The variable sequence segment in the cp26 plasmids of K78 is compared with 25 Borrelia strains. A maximum likelihood tree rooted with a B. bissettii sequence as outgroup, shows the relationship for the intergenic part, which in B. afzelii K78 is situated between BAFK78_A0014 and BAFK78_A0015 (bacterial extracellular solute-binding protein), and which shows a species-specific length. Insertions and deletions within this region have been analyzed with the program Mauve, and the compositional analysis for 16 of the 26 sequences (underlined in the tree view) is shown with related segments marked by color and/or boxes together with a similarity score diagram for each sequence. Blue bars denote segments which, in some strains, have been annotated as short hypothetical proteins (the number of assigned proteins in this region is indicated in parentheses in the tree view).