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Table 3 Plasmids present in B31-NRZ, PAli and PAbe

From: Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi

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)

  1. aBbss = B. burgdorferi s.s.; the full complement of B31-GB plasmids can be found in Table S3
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
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