Table 3.
Plasmids present in B31-NRZ, PAli and PAbe
| GenBank | PCR verification | PacBioscience SMRT sequences | ||
|---|---|---|---|---|
| B31 or other Bbssa strains | B31 NRZ | B31 NRZ | PAli | PAbe |
| cp26 | cp26 | cp26 (con9) | cp26 (con6) | cp26 (con8) |
| cp32-1 | cp32-1_i5_i6 (con4)b
(61,436 bp) |
cp32-1c (con14) cp32-1_i6 (con15) |
cp32-1_i5_i6d (con2) (56,633 bp) | |
| cp32-3 | cp32-3 | cp32-3 (con8) | cp32-3 (con4) | cp32-3 (con5) |
| cp32-4 | cp32-4 (con10) | cp32-4 (con9) | (fusion cp32-9) | |
| cp32-2 | cp32-2 (con6)e | - | cp32-2 (con6)e | |
| cp32-5 | (fusion cp32-1) | cp32-5 (con13) | (fusion cp32-1) | |
| cp32-9 | cp32-9 (con7) | cp32-9 (con7) | cp32-9 (con3)f
(62,240 bp) |
|
| lp17 | lp17 | lp17 (con5) | lp17 (con8) | lp17 (con7) |
| lp28-1 | lp28-1g | lp28-1 (con12, 21,885 bp) | - | lp28-1 (4800 bp) |
| lp36 | lp36 | lp36 (con11) | lp36 (con5) | lp36 (part; con11: 2313 bp; con12: 10,472 bp; con20: 2825 bp; con22: 3.932 bp) |
| lp38 | lp38 | lp38 (con2) | lp38 (con10) | - |
| lp54 | lp54 | lp54 (con1) | lp54 (con2) | lp54 (con1) |
| lp56 | lp56 | lp56 (con3) | lp56 (con3) | lp56 (con42: 10,951 bp, con43: 48,674 bp; overlap 200 bp) |
aBbss = B. burgdorferi s.s.; the full complement of B31-GB plasmids can be found in Table S3
bIn B31-NRZ contig4 (con4) of the SMRT sequences was likely a hybrid plasmid as the first app. 33,000 bp showed 1138 SNPs to cp32-1 while the sequence starting from 33,000 had 773 SNPs to cp32-1. The regions showing variation to cp32-1 of B31 showed similarity to cp32-5 of strain 64b (21–26 kb) and to cp32-6 of strain 156a (47–48.5 kb) (see text for details). Contig4 had 6631 SNPs compared to cp32-1 + 5 of JD1. Its PFam32 sequences showed 100% similarity to cp32-5 and cp32-1
cIn PAli, three contigs were found that matched cp32-1 in BLAST searches. Contig14 showed 20 SNPs to cp32-1 but was short (20,004 bp) and did not have a PFam32 locus. Contig13 matched cp32-1 from 1 to 18,740 bp, 18.7–23 kb the similarity was higher to cp32-5 of B. burgdorferi s.s. strain 64b , while the remaining sequence to 32,285 matched cp32-1 again. Its PFam32 sequences showed 100% similarity to cp32-5 of several B. burgdorferi s. s. strains. Contig15 between 16.5 and 18 kb showed a closer match to cp32-6 of strain 156a while the remaining sequence matched cp32-1. PFam32 sequence of contig15 was identical to cp32-1 of B31-GB
dIn PAbe one contig was present (contig2) that partially matched cp32-1 but part of the sequence also matched cp32-5 (appr. 14.5–19 kb) and cp32-6 (appr. 40–42 kb). In contig2, the PFam32 of cp32-1 showed 100% identity
eA plasmid was found in B31-NRZ that was not present in the B31-GB reference. Its PFam32 sequence was identical to cp32-2 and showed high similarity (99%) to cp32-7 of several B. burgdorferi s.s. strains. An almost identical plasmid was found in PAbe with a PFam32 matching that of cp32-2
fIn BLAST searches contig3 of PAbe showed similarity to cp32-9 . However, the first part of the sequence was highly similar to cp32-9 while the second part was more similar to cp32-4 of B31 suggesting that this plasmid represents a hybrid plasmid. The PFam32 sequences were identical to PFam32 of cp32-9 and cp32-4
gIn B31 plasmid lp28-1 is short (21,885 bp). In PAbe the presence of lp28-1 is questionable as there were only two contigs of approximately 4800 bp that showed high similarity to lp28-1