supplementary material table of contents10.1186...additional file 1 casjens et al. 1 supplementary...

Additional file 1 Casjens et al.

1

Supplementary Material Table of Contents Figure legends Figure S1. Borreliella plasmid PFam32 protein neighbor-joining tree ..................................... 2 Figure S2. Two examples of Borreliella linear plasmids with low protein coding potential 2 Figure S3. Comparative maps of linear plasmids in Lyme agent Borreliella isolates ............ 3 Figure S4. The PFam54 gene cluster of the Borreliella lp54 plasmids ...................................... 4 Figure S5. Ends of the Borreliella linear chromosome sequences ............................................. 4 Figure S6. Comparative maps of cp9 plasmids in Lyme agent Borreliella isolates ................ 5 Figure S7. Orphan cp32-like contigs in the B. spielmanii A14S genome .................................. 5 Figure S8. Rearrangements in cp32-like plasmids in NBu-Borreliella genomes ..................... 6 Figure S9. B. bissettiae DN127 66 kbp circular plasmid cp32-quad .......................................... 6 Figure S10. B. finlandensis SV1 integration of cp32 into lp54 ..................................................... 6 Figure S11. Borreliella and relapsing fever Borrelia PFam32 protein neighbor-joining tree ... 7

Tables Table S1. Lyme agent Borreliella sequence accession numbers .................................................8-9

References ............................................................................................................................. 10-11

Figures Figure S1 .......................................................................................................................................... 12 Figure S2 .......................................................................................................................................... 13 Figure S3 A-L .............................................................................................................................. 14-25 Figure S4 ........................................................................................................................................... 26 Figure S5A-B ............................................................................................................................... 27-28 Figure S6 .......................................................................................................................................... 29 Figure S7 .......................................................................................................................................... 30 Figure S8 .......................................................................................................................................... 31 Figure S9 .......................................................................................................................................... 32 Figure S10A-B ................................................................................................................................. 33 Figure S11 ........................................................................................................................................ 34


2

Figure S1. Borreliella plasmid PFam32 protein neighbor-joining tree. PFam32 amino acid sequences were aligned and an unrooted neighbor-

joining tree was constructed by Clustal X (Larkin et al., 2007) showing the different PFam32 branches highlighed with different colors; bootstrap values from 1000 trials are shown above the branches and branches with bootstrap values below 900 are collapsed to multi-branch points. A fractional distance scale bar is shown at the lower left. All currently known PFam32 protein types from the Borreliella species are shown; in some types only several representative B. burgdorferi were included to simplify the tree. Plasmid names are indicated at the right of each branch in large text, and Borreliella isolates carrying them are indicated in smaller text at the branch tips. The asterisks (*) note the unusual second PFam32 protein encoded on strain B31 plasmid lp28-1 and the PFam32 genes present in small contigs of draft B. afzelii PKo and B. japonica HO14

genomes sequences (see text of article); the larger stars (★) mark the DN127 lp56 and Bol26 lp28-9 plasmids whose phylogenetic positions are inconsistent with the genome tree in figure 5 of the text. Lepto_ParA denotes the chromosomally encoded ParA protein from Leptospira interrogans strain UT126, a species in another spirochete genus.

Figure S2. Two examples of Borreliella linear plasmids with low protein

coding potential. Plasmid lp28-4 from strain PKo and plasmid lp36 from strain A14S are shown

as reading frame maps are shown with the six possible reading frames (top three rightward frames and bottom three leftward); stop codons are indicated by vertical lines that span the frame rectangle, and potential start codons are indicated by short vertical lines. ORFs that appear to be intact are green, apparent pseudogenes are red, and small ORFs called by our annotation pipeline or by manual observation that may or may not be functional genes are yellow. The maps were created with DNA Strider (Douglas, 1994) and colored with Adobe ILLUSTRATOR. Paralogous protein family (PFam) numbers are given above where asterisks (*) mark the pseudogenes. Locus_tags (e.g., BB_K19) identify homologous proteins that do not belong to a PFam.


3

Figure S3. Comparative maps of linear plasmids in Borreliella isolates. Linear plasmid reading frame maps are shown with the six possible reading

frames (top three are rightward frames and bottom three leftward) with stop codons indicated by vertical lines that span the frame rectangle, and potential start codons are indicated by short vertical lines (created with DNA Strider; Douglas, 1994). Green shading between maps indicates most of the homologous regions among adjacent plasmids. In each panel, the same shading color on the maps indicates regions of similar sequence. In appropriate cases, representative B. burgdorferi plasmids are included for comparison.

Maps of the following linear plasmids are shown in the figure panels: A, lp5; B, lp17; C, lp25; D, lp28-2, lp28-7 and lp28-9; E, lp28-3; F, strain VS116 lp28-3; G, lp28-4; H, lp28-8; I, lp32s; J, lp36; K, lp38; L, lp56.

Plasmid names are shown at the top of each panel and strain names at the left. Plasmid subtype Roman numeral names are indicated at the right in black with the species name in red text. Above the maps selected PFam numbers or names of homologous genes are shown (Paralogous Protein Families defined by Casjens et al. (2000, 2012); note that original related PFams 62 and 57 are merged into one PFam57. Asterisks (*) indicate obvious truncated or frame-disrupted pseudogenes, and hash marks (#) indicate draft sequences.

A “U” above an ORF marks a NBu-Borreliella protein that has no homologues on the B. burgdorferi linear plasmids. These are typified by the following examples: U1 B. afzelii isolate BO23 lp17 locus_tag BLA32_05550 - unique in sequenced

plasmids U2 B. afzelii isolate PKo lp17 locus_tag BafPKo_D0023 and homologues U3 B. afzelii isolate ACA-1 lp17 locus_tag BafACA1_D03 and homologues;

unannotated pseudogene "homologue" present in B. burgdorferi lp17. U4 B. garinii isolate PBr lp25 locus_tag BGAPBR_E0006 and homologues U5 B. spielmanii isolate A14S lp28-8 locus_tag BSPA14S_N0008 and

homologues U6 B. spielmanii isolate A14S lp36 locus_tag BSPA14S_K0035 and homologues


4

U7 B. afzelii isolate PKo lp28-8 locus_tag BafPKo_AC0001; homologues of unknown function found adjacent to sagE in other species (Molloy et al., 2015) and so sometimes called sagF.

U8 B. afzelii isolate PKo lp32-10 locus_tag BafPKo_Q0008 - unique in sequenced plasmids

U9 B. afzelii isolate PKo lp38 BafPKo_J0009 and homologues Figure S4. The PFam54 gene cluster of the Borreliella lp54 plasmids.

The cluster of PFam54 genes that all lp54 plasmids carry a near their right ends is shown for all the Borreliella isolates for which they have been sequenced. Individual genes are depicted as bars whose pointed ends indicate the direction of transcription. The cluster is bounded by black vertical lines in the figure, and blue vertical lines bound the central much more variable region. Individual isolates are indicated on the left, and species with lp54 subtype in Roman numerals is indicated on the right. All the PFam54 genes are related to some degree, and in the variable region genes of the same color form groups that are ≥65% identical in amino acid sequence. A few outliers just outside that limit are indicated above the gene with the percent identity to the rest of the group. The rightmost identifying portion of their GenBank locus-tags are shown on each gene, asterisks (*) denote the longer pseudogenes that are truncated or have reading frame disruptions, and the red triangle in the B. finlandensis line indicates the site of cp32 integration. Spaces between genes in the variable region do not indicate the presence of DNA, but only serve to allow better vertical alignment of the different gene types indicated by the different colors. Black X's mark regions that have not yet been sequenced. Figure S5. Ends of the Borreliella linear chromosome sequences.

Maps of the sizeable ORFs at the left and right end regions of the linear chromosomes of the available NBu-Borreliella sequences are shown in parts A and B, respectively. Two B. burgdorferi termini are shown for comparison. Predicted genes are shown as rectangles with pointed ends that indicate the direction of transcription and the B31 gene names are indicated on the B31 maps.


5

Heavy black horizontal lines mark the extent of the terminal sequence. Green genes are in terminal extensions relative to the common short chromosomes; the paralogous protein family (PFam abbreviated here as PF) is given above each such gene and small asterisks (*) mark pseudogenes. Numbers above each map give the bp lengths of common chromosomal genes (including the stop codon), distance between genes (a negative value for the latter indicates a postulated gene overlap), and distance from the most terminal common gene (bb_001 at left end except for the B. valaisiana strains where it is bb_002; bb_843 at right end) to the end of the sequence. Parentheses mark the inversion in Tom4006 relative to VS116. Scales in kbp are shown above that begin at the start of the indicated gene.

We note that because the linear Borreliella replicons have closed hairpin telomeres, their terminal fragments are not ligated into plasmid DNA libraries. Thus, sequences determined by dideoxy-sequencing of such libraries do not include the near terminal sequences. Sequences that include the telomere are marked with a large asterisk (*); black asterisks indicate telomeres that were purposefully sequenced, and gray asterisks indicate sequences that appear include at least most of the ~25 bp telomere sequence. Jagged termini of genes mark locations where such early sequencing methods did not reach the end of the terminal gene.

Figure S6. Comparative maps of cp9 plasmids in Borreliella isolates.

Aligned open reading frame maps were created as described for figure S3. Asterisks (*) indicate the accession numbers for two putative A14S contigs that were not "closed". They are very likely to be cp9 contigs because of their unique high similarity to the cp9s of other Borreliella species.

Figure S7. Orphan cp32-like contigs in the B. spielmanii A14S genome.

Strain A14S nucleotide sequence contigs are shown as horizontal bars that are aligned with homologous sequences in the strain B31 cp32-1 plasmid. The cp32-1 plasmid is circular (opened for linear display here at an arbitrary point as in accession number AE001575), and its six frame open reading frame map (created as described for figure S3 by DNA Strider; Douglas, 1994) is shown above.


6

Homologies for two contigs, ABKB02000023 and ABKB02000034 cross the location at which the map was opened; however, this homology is only indicated at one end of the map. The location of the cp32-1 PFam32 gene (see article text) is indicated in green on the map and contig bars that encode whole or parts of PFam32 gene are colored green.

Figure S8. Rearrangements in cp32-like plasmids in non-burgdorferi Borreliella genomes.

An ORF map (see figure S3) of strain B31 cp32-1 is shown above for comparison, and the NBu-Borreliella cp32s with long rearrangements are indicated by magenta bars below; long deletions are indicated by thin magenta lines and insertions and replacements by thick blue bars. The variable regions shown above the map were discussed and defined by Casjens et al. (2012). The ancient triplication that created PFam148 (marked in purple above; see text) includes strain B31 cp32-1 genes bb_p03, bb_p04 and bb_p05.

Figure S9. B. bissettiae DN127 66 kbp circular plasmid cp32-quad.

ORF maps (see figure S3) of strain DN127 cp32-quad and cp32-7 are shown along top and right axes for orientation. The indicated section of the cp32-quad sequence was manually inverted so that all the internal sequence similarities could be displayed in one plot. The dot plot was created by DNA Strider (Douglas, 1994) with a scan window of 13 identities in 15 bp. The location of PFam32 protein encoding genes are indicated above.

Figure S10. B. finlandensis SV1 integration of cp32 into lp54.

A. A dot plot that compares strain B31 lp54 and SV1 lp54 is shown that was created by DNA Strider (Douglas, 1994) with a scan window of 17 identities in 23 bp. Similar comparison of SV1 lp54 to a cp32 plasmid showed the location of the cp32-11 sequence in this lp54 (indicated by the yellow bar). The B31 lp54 ORFs are indicated below the plot.

B. The putative sequences of the parental lp54 and cp32 plasmids are shown. The nonhomologous crossover point that generates the SV1 fused plasmid is marked by a carat (^).


7

Figure S11. Borreliella and relapsing fever clade Borrelia PFam32 protein

neighbor-joining tree. The tree was constructed as in figure S1. The relapsing fever PFam32

proteins, indicated by “species_strain name_plasmid name” at their branch tips, and the branches on which they reside are colored red (note that among these plasmids only B. recurrentis A1 plasmid pL53 encodes two such proteins). The Borreliella PFam32 plasmid types are indicated in large black text at the right of the black branches. All known PFam32 protein types from the Borreliella species are shown; in some types only several representative B. burgdorferi were included to simplify the tree.


8

Table S1

Borreliella sequence accession numbers Part 1. Accession numbers of anecdotal plasmid sequences listed in figure 1

B. afzelii B. garinii B. japonica Strain BO23 20047 HO14 Plasmid

cp9 CP018274 – – cp26 CP018266 CP018750 FMTE01000007 lp17 CP018269 CP018751 – lp25 – – FMTE01000009 lp28-3 CP018265 – – lp28-4 CP018268 – – lp28-7 CP018267 CP018749 – lp28-8 CP018264 – FMTE01000008 lp36 – CP018746 – lp38 CP018263 – – lp54 CP018263 CP018745 FMTE01000005

Part 2. Accession numbers of plasmid sequences not listed in figure 1

Plasmid cp9(cp8.3) cp26 lp54 Species / Isolate B. afzelii Tom3017 – NZ_CP009213 NZ_CP009214 MMS – – AJ786368 a B. bavariensis PBi – CP000014 CP000015 BgVir – CP003201 CP003202 ZQ1 – – AJ786369a B. garinii Ip21 U03641 – – B. valaisiana Tom4006 – NZ_CP009118 NZ_CP009119 B. chilensis VA1 – CP009911 CP009912


9

Table S1 (cont.)

Part 3. Accession numbers of chromosomes Species / Isolate Chromosome Reference

B. afzelii Tom3017 NZ_CP009212 (Kurilshikov et al., 2014) HLJ01 CP003883 (Jiang et al., 2012b) R-IP3 AF008219 (Casjens et al., 1997) B. bavariensis PBi CP000013 (Glöckner et al., 2004) BgVir CP003151 (Brenner et al., 2012) SZ CP007564 (Wu et al., 2014) NMJW1 CP003866 (Jiang et al., 2012a) B. burgdorferi B31 AE000783 (Fraser et al., 1997) Sh-2-82 AF008218 (Casjens et al., 1997) B. valaisiana Tom4006 NZ_CP009117 (Kurilshikov et al., 2014)

B. chilensis VA1 CP009910 (Huang et al., 2015)

Footnote

a. Only the PFam54 cluster sequence is known; see figure S4


10

Supplementary Material References Brenner, E. V., Kurilshikov, A. M., Stronin, O. V., Fomenko, N. V., 2012. Whole-

genome sequencing of Borrelia garinii BgVir, isolated from Taiga ticks (Ixodes persulcatus). J Bacteriol 194, 5713.

Casjens, S., Murphy, M., DeLange, M., Sampson, L., van Vugt, R., Huang, W. M., 1997. Telomeres of the linear chromosomes of Lyme disease spirochaetes: nucleotide sequence and possible exchange with linear plasmid telomeres. Mol. Microbiol. 26, 581-96.

Casjens, S., Palmer, N., van Vugt, R., Huang, W. M., Stevenson, B., Rosa, P., Lathigra, R., Sutton, G., Peterson, J., Dodson, R. J., Haft, D., Hickey, E., Gwinn, M., White, O., Fraser, C. M., 2000. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol Microbiol 35, 490-516.

Casjens, S. R., Mongodin, E. F., Qiu, W. G., Luft, B. J., Schutzer, S. E., Gilcrease, E. B., Huang, W. M., Vujadinovic, M., Aron, J. K., Vargas, L. C., Freeman, S., Radune, D., Weidman, J. F., Dimitrov, G. I., Khouri, H. M., Sosa, J. E., Halpin, R. A., Dunn, J. J., Fraser, C. M., 2012. Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids. PLoS One 7, e33280.

Douglas, S. E., 1994. DNA Strider. A Macintosh program for handling protein and nucleic acid sequences. Methods Mol. Biol. 25, 181-94.

Fraser, C. M., Casjens, S., Huang, W. M., Sutton, G. G., Clayton, R., Lathigra, R., White, O., Ketchum, K. A., Dodson, R., Hickey, E. K., Gwinn, M., Dougherty, B., Tomb, J. F., Fleischmann, R. D., Richardson, D., Peterson, J., Kerlavage, A. R., Quackenbush, J., Salzberg, S., Hanson, M., van Vugt, R., Palmer, N., Adams, M. D., Gocayne, J., Venter, J. C., 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390, 580-6.

Glöckner, G., Lehmann, R., Romualdi, A., Pradella, S., Schulte-Spechtel, U., Schilhabel, M., Wilske, B., Suhnel, J., Platzer, M., 2004. Comparative analysis of the Borrelia garinii genome. Nucleic Acids Res 32, 6038-46.

Huang, W., Ojaimi, C., Fallon, J. T., Travisany, D., Maass, A., Ivanova, L., Tomova, A., Gonzalez-Acuna, D., Godfrey, H. P., Cabello, F. C., 2015. Genome Sequence of Borrelia chilensis VA1, a South American Member of the Lyme Borreliosis Group. Genome Announc 3, e01535-14.

Jiang, B., Yao, H., Tong, Y., Yang, X., Huang, Y., Jiang, J., Cao, W., 2012a. Genome sequence of Borrelia garinii strain NMJW1, isolated from China. J Bacteriol 194, 6660-1.

Jiang, B. G., Zheng, Y. C., Tong, Y. G., Jia, N., Huo, Q. B., Fan, H., Ni, X. B., Ma, L., Yang, X. F., Jiang, J. F., Cao, W. C., 2012b. Genome sequence of Borrelia afzelii Strain HLJ01, isolated from a patient in China. J Bacteriol 194, 7014-5.

Kurilshikov, A. M., Fomenko, N. V., Stronin, O. V., Tikunov, A. Y., Kabilov, M. R., Tupikin, A. E., Tikunova, N. V., 2014. Complete Genome Sequencing of Borrelia valaisiana and Borrelia afzelii Isolated from Ixodes persulcatus Ticks in Western Siberia. Genome Announc 2, e01315-14.


11

Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G., 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-8.

Molloy, E. M., Casjens, S. R., Cox, C. L., Maxson, T., Ethridge, N. A., Margos, G., Fingerle, V., Mitchell, D. A., 2015. Identification of the minimal cytolytic unit for streptolysin S and an expansion of the toxin family. BMC Microbiol 15, 141.

Wu, Q., Liu, Z., Li, Y., Guan, G., Niu, Q., Chen, Z., Luo, J., Yin, H., 2014. Genome Sequence of Borrelia garinii Strain SZ, Isolated in China. Genome Announc 2, e00010-14.

lp21

lp56

lp28-1

lp28-6

lp17

lp28-7

cp32-4

lp36

lp28-2

cp32-13

cp26

cp32-3

lp28-9

lp28-8

cp32-8

cp32-10

cp32-5

cp32-6

lp25

lp28-5cp32-9

lp54

cp9cp32-1

cp32-7

lp28-3

?Lepto_ParA

B31_lp21156a_lp21

N40_lp36B31_lp36

MN13-1420_lp36MN13-1539_lp36

29805_lp3620047_lp36PBr_lp36Far04_lp36

VS116_lp36A14S_lp36

1000

B31_lp28-329805_lp28-3

Bol26_lp28-3MN14-1420_lp28-3MN14-1539_lp28-3

PBr_lp28-3DN127_lp28-3

ACA-1_lp28-3K78_lp28-3A14S_lp28-3PKo_lp28-3BO23_lp28-3

VS116_lp28-3

BB31_lp28-1_F13*

1000

JD1_lp28-6297_lp28-6

1000CA11_lp56DN127_lp56

WI91-23_lp56B31_lp56

B31_lp38N40_lp38

WI91-23_lp38JD1_lp38K78_lp38PKo_lp38

ACA-1_lp38BO23_lp38

A14S_lp38

1000

1000

B31_lp28-1WI91-23_lp28-1JD1_lp28-1297_lp28-1

K78_lp28-1ACA1_lp28-9PBi_lp28-9Bol26_lp28-9

PBr_lp28-9Far04_lp28-9

1000

100072a_cp32-13118a_cp32-13CA11_cp32-13MN14-1420_cp32-13MN14-1539_cp32-13

DN127_cp32-131000MN14-1420_cp32-4MN14-1539_cp32-4B31_cp32-4

N40_cp32-4297_cp32-4

DN127_cp32-4SV1_cp32-4

K78_cp32-4ACA-1_cp32-4

1000

1000JD1_lp28-7DN127_lp28-7

PBr_lp28-720047_lp28-7ACA-1_lp28-7

PKo_lp28-7BO23_lp28-7

1000

997

B31_lp28-2N40_lp28-2

ACA1_lp28-2K78_lp28-2

SV1_lp28-2PKo_lp28-2

1000

1000B31_cp26N40_cp26

JD1_cp26SV1_cp26MN14-1420_cp26MN14-1539_cp26

DN127_cp26ACA-1_cp26PKo_cp26

BO23_cp26K78_cp26Tom3107_cp26

PBi_cp26

PBr_cp2620047_cp26

Far04_cp26

A14S_cp26ATCC51557_cp26

VS116_cp26Tom4006_cp26

VA1_cp26N40_cp32-9

JD1_cp32-9B31_cp32-9

297_cp32-9DN127_cp32-9

K78_cp32-9PKo_cp32-9

1000

1000297_lp28-5JD1_lp28-5

N40_lp28-5MN14-1420_lp25MN14-1530_lp25

B31_lp25DN127_lp25JD1_lp25

VS116_lp25ATCC51557

PBr_lp25Far04_lp25

PKo_lp32-10ACA1_lp32-10PBr_cp32-10

Far04_lp32-10VS116_cp32-10

B31_cp32-10JD1_cp32-10N40_cp32-10

297_cp32-12JD1_cp32-12

DN127_cp32-12quadSV1_lp32-12

N40_cp32-12PKo_cp32-12

B31_cp32-8JD1_cp32-8

998

1000

100094a_lp28-8VS116_lp28-8

A14S_lp28-8PKo_lp28-8K78

BO23_lp28-8ATCC51557_lp28-8

MN14-1420_lp28-10MN14-1539_lp28-10

B31_cp32-5JD1_cp32-5

DN127_cp32-5VS116_cp32-5

PBr_cp32-5PKo_cp32-5ACA1_cp32-5

K78_cp32-5A14S_cp32-5

N40_lp28-4B31_lp28-4WI91-23_lp28-4SV1_lp28-4

MN14-1420_lp28-4MN14-1539_lp28-4

DN127_lp28-4PBr_lp28-4A14S_lp28-4PKo_lp28-4K78_lp28-4ACA1_lp28-4BO23_lp28-4

1000

1000

JD1_cp32-6B31_cp32-6

SV1_lp32-6DN127_cp32-6

MN14-1420_cp32-6MN14-1539_cp32-61000

118a_lp32-372a_lp32-3B31_cp32-3MN14-1420_cp32-3MN14-1539_cp32-3

297_cp32-3K78_cp32-3ACA1_cp32-3PKo_cp32-3

SV1_cp32-3A14S_cp32-3

DN127_cp32-3CA-11_cp32-3

JD1_cp32-11297_cp32-11

PKo_cp32-11DN127_cp32-11

SV1_cp32-11

1000

1000B31_cp32-7N40_cp32-7SV1_cp32-7DN127_cp32-7

PKo_cp32-7VS116_cp32-7

Mayonii1539_cp9Mayonii1420_cp9DN127_cp9

BO23_cp9A14S_cp9

VS116_cp9

B31_cp32-1297_cp32-1MN14-1420_cp32-1MN14-1539_cp32-1

PKo_cp32-1ACA1_cp32-1

999

1000

1000

1000

VA1_lp54B31_lp54297_lp54JD1_lp54N40_lp54

SV1_lp54Far04_lp54BPr_lp54

20047_lp54BgVir_lp54

PBi_lp54Tom4006_lp54VS116_lp54

MN14-1420_lp54MN14-1539_lp54

DN127_lp54ATCC51557_lp54A14S_lp54

Tom3107_lp54PKo_lp54BO23_lp54K78_lp54ACA1_lp54

1000

1000

1000

1000

1000

930

998

953

924

930

PBr_lp17

Far04_lp17PBi__lp17VS116_lp17

PKo_lp17ACA1_lp17BO23_lp17K78_lp17A14S_lp17

SV1_lp17DN127_lp17

MN14-1420_lp17MN14-1539_lp17

B31_lp17N40_lp17

20047_lp17

1000

0.11000

cp32-11

lp28-4

lp38

cp32-12

Figure S1

HO14_SAMN02983004_01117*PKo_BAPKO_2556* ?1000

1000

page 12

**

2 4 6 8 10 12 14 16 18 202 4 6 8 10 12 14 16 18 20 22 Kbp

3>2>1><1<2<3

60

BB_I18*

60 49325057

B31_I18*80*

sagD frag

12*

138

113*

01

95*163* 163*

PKo lp28-4

60*

24 26 28 29 Kbp

3>2>1><1<2<3

A14S lp36

4932 50 57

44*01* U1

82*TPase

6865*

40

BB_K32*fibronectin binding protein 48*

6012* 26 61adeC

BB_K19

U2

2 4 6 8 10 12 14 16 18 20 22

102**

Figure S2

page 13

99.98%

B31

WI91-23

lp5

1 2 3 4 5 Kbp

99.69%

Figure S3A

13757* 57* 84 57* 52*

mayonii

burgdorferi

MN14-1420

page 14

57

57

50 8880

ACA-1

21 bp - 20 Reps

N40

B31

PKo

PBr, Far04, 20047B31 lp38 synteny

VS116

DN127

B31 lp36 synteny

bissettiae

valaisiana

garinii

afzelii

burgdorferi

B31 lp28-2 synteny

I

II

lp17

A14S K78

spielmanii afzelii

VIB31 lp28-3

2 4 6 8 10 12 14 16 18 20 22 24 Kbp

I

II

bb_k

32

ospD

cspZ

SV1 finlandensis

Figure S3B

60*

106 04 59

82

69 75

12

60

60*

60

5454

54 12

12

75 54

52 44

mayoniiMN14-1420MN14-1539

156a lp38 synteny 92% identity

54 3201*

Far04 lp32-10 synteny

ACA-1 lp28-4 synteny 99% identity

IIIB023

54

U1

U3

U2

WI91-23

76 57* 82*3257bb_d

09

bb_d

10

bb_d

11

bb_d

18

57

I

I

I

I

I

I

55

68

82

82*

page 15

Partition Genes

B31, ZS7, 29805

lp25

JD1, 118a,156a

I

III

pncA

VS116

86% B31 lp28-4 84% B31 lp38

96 02* 96 JD1_

j07105*

PBr

80 88

54

402660 105

adeC

60

Far04

burgdorferi

garinii

valaisiana

DN12754

bissettiae

I

II

Figure S3C

long tandem duplication

mayoniiMN14-1420MN14-1539

1000 2000 3000 4000 5000 6000 7000 8000 9000 10K 11K

japonicaHO14

9944 12bb_k

32

BbuJD

1_j07

bptA

01 50324944 60

128246* 102

99 57bptA

pncA

82*

bb_e

17

bb_e

17

U4

61

2 4 6 8 10 12 14 16 18 20 22 24 Kbp

FMTE01000009 #

I

I

I

I

pncA

page 16

lp28-2, -7 & 9

Bol26

afzelii

Far04

ACA-1

44 885086167 50 5726 102 104101 57* 57* 80

PBr20047

B31

ACA-1

PKo, K78

SV1

K78

vls cassettes

DN127

PKo

BO23

PBr

JD1

lp28

-2lp

28-9

lp28

-7

finlandensis

burgdorferi

burgdorferi

burgdorferi

garinii

garinii

afzelii

bissettiae

B31 lp25 ~85%

57

8046103117 8886 57

57

76

50*104

52 99bptA

10182*10212 3250 4957 86

pncA

170 102* 6950

57

101

82

167

59

57

57

B31_K32

57*

adeC59

48

163

80

8052

B31_K19

50

82

46

82

95

12 32 5049 57

80

95 32 5049 57

vlsE

B31 lp36 ~95%

180plzB

61

88

57*

ACA-1

afzelii

01

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 Kbp

PBr

jd1_J

07

12

II

III

I

I

I

I

II

I

I

I

II

I

I

I

II

??

Figure S3D

50 bb_e

17

bb_k

19

page 17

lp28-3 Figure S3E

B31

vls cassettes

01cspZ 69 126080 4850 493262

PKo, ACA-1, K78

BO23

PBr

A14S

DN127

MN14-1420MN14-1539

VS116

Partition genes

163 5449 32* 50 26 10560

52

52

54

82*

105

44

44

105*

163

163

60

54

44

ospD

170

44

111

6012 60

68* 60*

44 1292cspZ

01*

bissettiae

valaisiana

burgdorferi

spielmanii

mayonii

afzelii

garinii

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 Kbp

46 kbp not shown(see VS116 lp28-3 map in Figure S3F)

vlsE

cp32 homology

83%

I

I

I

I

I

I

I

II

page 18

2000 4000 6000 8000 10K 12K 14K 16K 18K 20K 22K 24K 26K 28K 30K 32K 34K 36K 38K 40K 42K 44K 46K 48K 50K 52K 54K 56K 58K 60K 62K 64K 66K 68K 70K 72K 74K 76K 78K 80K 82K

Partition Genes

B. valaisiana VS116 lp28-3

Figure S3F

141vlsE

B31 lp38 homologyB31 lp38 homology cp32 homology PBr lp28-4 homology

PBr lp28-4 homology

PBr lp36 homology PBr lp36 homology

60 5426 105

lp28-4 type PFam32

4932

50B31_J2

5

60 6901* 80152 90106138142574932*

5095* 106

B31_J26

B31_J28

B31_J27

sagD*32*

lp38 type PFam32

32* BVAVS116_H0114-B31-K32*

page 19

B31

lp28-4Figure S3G

105 54 54606050 49325726 60Partition genes

SV1

DN127

MN14-1420MN39-1439

PKo, ACA-1, K78

PBr

A14S

PBr lp25 - 99% PBr lp36 - 94%

A14S lp36 - 94%PKo lp32-10 - 94%

vlsE

50

76*59

80 40

926060944417054*U4105

12*13860

12B31_J074910501

015260105*6052

40*60*6060

54 52

cspZ

(B023 circularly permuted and is thus subtype II)

B31_J07

2K 4K 6K 8K 10K 12K 14K 16K 18K 20K 22K 24K 26K 28K 30K 32K 34K 36K Kbp

bissettiae

finlandensis

burgdorferi

spielmanii

mayonii

afzelii

garinii

I

I

I

I

I

I

I

page 20

lp28-8vls cassettes01 98

Partition genes

90*JD1_

j07

62*

99% to lp38 sensu stricto subtypes IV & V

PKoK78

VS116

A14S

94a

92.0%

92.0%

60 82* 503249

54

57

48 cpsZ

MN14-1420*MN14-1539*

Figure S3H

vls cassettes

vls cassettes

vls cassettes

vls cassettes

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Kbp

vlsE170

10.6. kbp vls cassettes not shown

1061060490sagEDCBAU7 B31_J

25

B31_J

28

B31_J

27

valaisiana

burgdorferi

spielmanii

mayonii

afzelii

japonica

BO23

HO14

vlsE???1708088 75 54 vls cassettes

vls cassettes

* Figure includes B. mayonii “lp28-10s” (see text)

I

II

I

I

I

I

I

page 21

118a

lp32-3, -6, -10 & -12Figure S3I

lp32

-6lp

32-1

2lp

32-1

0

PKo

ACA-1

Far04

lp32

-3 106 57*

32

32

Partition genes

vls cassettes57508049 14450 16332

vls cassettes

SV1

SV1

cp32 homologycp32 homloogy

cp32 homloogy

cp32 homology

cp32 homology

cp32 homology

# The two contigs of the SV1 plasmid lp32-6 were not “closed” but were experimentally connected to the same plasmid; the gap was not sequenced

Yellow shading marks regions that have similarity to strain 118a plasmid lp32-3. This largely marks the partition gene clusters which, although they have some similarity, encode PFam32 proteins of dfferent types in the different types of plasmid.

ABJZ02000007#ABJZ02000006#151 159

111

U8 138

cspZ

88

57*

76

102/167 80

7554ospD

15614912

106 5401*

92

01*

2000 4000 6000 8000 10K 12K 14K 16K 18K 20K 22K 24K 26K 28K 30K 32K 34K 36K 38K 40K 42K 44K 46K 48K 50K Kbp

burgdorferi

finlandensis

afzelii

garinii

finlandensis

PKo lp17 96%

52 8248

57

495057

495057

page 22

B31, 64b, Bol26, ZS7

I

lp36Partition Genes

Far04

PBr

A14S

VS116 valaisiana

garinii

burgdorferi

spielmanii682612

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 34 Kbp32

K01K12

K15K17

K21 K23

K32

K45 K47 K48K49 K50

K52K07

Figure S3J

MN14-1420MN14-1539

20047

mayonii

82102* 69 126080 01170

138

59

40

54

605057401056012

605744

49 105 88*

46

vlsE

57 4932

54

5801*adeC

75

50

69 75 69 75 445912

U6 U5

adeC

adeC

88

B31_K

19

B31_K

19

170vlsE

8232

6160 B31_K

19

60 61

B31_K

32

70

B31_K

32*

50

I

II

I

III

I

I

61

page 23

B31

156a

VI

IV

I

lp38

JD1

Partition Genes

Figure S3K

PKo, ACA-1, K78(B023 lp38-lp54 fusion constitutes subtype II)

A14SA14S lp36 99% Pko lp28-2 ~90%

57 bb_j2

54982* 484 52*59ospD12 50 1063260* 999054925990bb

_j27

10648* 170*bb_j2

892

26 5212 52

111

adeC

92 01

137

60

5257*pncA

23* 60

U6 99

U9

68

60

105*

60

52

Jjd1_

j07

bb_k

15

bb_e

17

60 105*

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 Kbp

burgdorferi

spielmanii

afzelii

I

IbptA

page 24

lp56

III

II

IVWI91-23

CA-11.2a DN127

94a

Partition Genes

93% 118a lp28-6 92% B31 lp28-2

97% 118a lp28-6

95% ZS7 lp28-2

Figure S3L

01 86

12

52 60

86

49 32 5750

101 104

102 167

4662 80 8850

2 4 6 8 10 12 14 16 18 20 22 24 26 Kbp

bissettiae

burgdorferi

burgdorferi

burgdorferi

page 25

PKo A0059 A0060 A0063A0061 A0062 A0064 A0065 A0066 A0067 A0068

A63 A64 A66A65 A67 A68 69 A71A70* A73A72PBi

297, N40, CA.11_2A72a, 94a, 118a, 156a, 29805, WI91-23

A64 A65 A68/cspAA66B31, Bol26, ZS7, 64a A69 A70 A73

A64 A65 A68A66JD1 A69 A73

A64 A65 A67.5A66 A68 A69 A73

a67a66 a68 a69 a70 a73a72a71ZQ1 X X

a67a66 a68 a69 a70 a71 a73MMS XX

Variable Regionlp54 PFam54 Gene Array

VA1 4665 4670 4675 469046854680

ACA-1 A65 A66 A67 A73A69A68 A72A71A70

K78 A060 A061 A062 A068A064A063 A067A066A065

PBr A0063 A0064 A0066 A0073A0068A0067 A0072A0071A0070

Far04 A0063 A0064 A0066 A0076A0073 / 4*A0069A0068 A0075A0072A0071

VS116 A0055 A0056 A0057 A0062A0058 A0060A0059* A0065A0064

Tom4006 4590 4585 4480 45404575 4565 4555 45454550

A057SV1 A108 A115A111A110A109 A114A112

cp32

20047 4550 4555 4560 460045804570 4595459045854565

Tom3107 4565 4560 4555 452045304550 4525453545404545

HO14 904 905 906 908907 909 X

MN14-1539 6225 6230 6235 6255625062456240

A0059 A0060 A0062A0061 A0061 A0064 A0065 A0066 A0068A0067DN12762%

A14S A0059 A0060 A0061 A0068A0063A0062 A0067A0066A0064

MN14-1420 4520 4525 4530 455045454540453562%

Figure S4

B. burgdorferi

B. bissettii

B. finlandensis

B. mayonii

B. afzelii

B. spielmanii

B. garinii

B. bavariensis

B. valaisiana

B. japonica

A0066

B. chilensis

X?

I

I

I

II

I

IIIIIII

I

I

I

I

I

I

I

IIIIII

II

BgVir 1015 1014 1012 1003100710101011 1005 / 4*1009 1008 II

III

63%

A71*

A71*

page 26

K78PKo

BO23

20047PBr

Far04

ACA-1

Tom3107HLJ01

MN14-1420

MN14-1420

DN127

SV1

VA1

573 14671029B31*

–13104

VS116Tom4006

Kbp 7 6 5 4 3 2 1

A14S

Lyme Agent Borrelia Chromosome Sequence Left Ends

burgdorferi

finlandensis

mayonii

spielmanii

garinii

bavariensis

valaisiana

bissettii

chilensis

bb_00390

573 14671029 –1372bb_003

90Sh-2-82

579 14671029 –1356bb_003

114fs

579 14671029 –1376bb_003

120

582 14701029 –1383bb_003

120

bb_003bb_002bb_001

*221

582 14701029 –1383bb_003

120

*221

576 14761020 –13114bb_003

75

* 576 14761020 –13113bb_003

75

* 576 14761020 –1387bb_003

75

576 14761020 –13117bb_003

75

* 576 14761020 –1397bb_003

75

576 14761020 –13100bb_003

75** 1399

579 14791020 –13112bb_003

102

* 579 14791020 –1365bb_003

107fs* 483 3481020 –13107 1103

PBi512 14791020 –13

bb_003107

BgVir341 14791020 –13

bb_003107

NMJW1SZ

579 14791020 –1395bb_003

116

537 14791020 –13bb_003

116

14791032 –131468bb_00314791032 –13170

bb_003588 14671020 –13118

bb_00351

afzelii

Figure S5A

PF12

*

page 27

987 271142249R-IP3 *987 209142249

*K78618

PKo

987 385142249BO23

984 11114254320047

984 35143PBr

984Far04

987 74449ACA-1

987 272142249Tom3107

987 354142249HLJ01

984 166142551MN14-1420 *984 166142551MN14-1420 *

984 141751DN127

984 81851SV1

984 130143139VA1

984 142551B31 *

7466

984 142551N40

984 8629142569VS116

984 8914142569Tom4006

9 87654321

984 225142239HO14

984 9549A14S

Lyme Agent Borrelia Chromosome Sequence Right Ends

bb_842 bb_843

984 43248PBi

984 131248BgVir

984 178142543NMJW1

984 92142543SZ

Figure S5B

10

burgdorferi

finlandensis

mayonii

afzelii

spielmanii

garinii

bavariensis

valaisiana

japonica

bissettii

chilensis

11 Kbp

PF60* bb_001PF26PF61*PF40 PF60* PF47

( )

345

page 28

PF12 PF1* PF138

N40

B31

118a

cp9

89.9% 97.0%

96.0%

II

III

I

87.4%

57 50 49 161 95 55 63 16596

575049

bissettiae32

valaisiana

mayonii

garinii

burgdorferi

ABKB02000020* ABKB02000016*

spielmanii

Figure S6

afzelii32

eppA

* A14S cp9 sequence not “closed”

92%

6395

49

eppA

500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 6500 7000 7500 8000 8500 bp

DN127

VS116

MN14-1420MN14-1539

Ip21

A14S*

BO23

I

I

I

I

I

I

page 29

1000 2000 3000 4000 5000 6000 7000 8000 9000 10K 11K 12K 13K 14K 15K 16K 17K 18K 19K 20K 21K 22K 23K 24K 25K 26K 27K 28K 29K 30K

3>2>1><1<2<3

ABKB02000033

ABKB02000030

ABKB02000015ABKB02000041 ABKB02000040

ABKB02000028

ABKB02000031

ABKB02000025

ABKB02000013

ABKB02000021

ABKB02000034

ABKB02000029

ABKB02000027

ABKB02000037

ABKB02000038

ABKB02000019

ABKB02000014

ABKB02000017

ABKB02000026

ABKB02000024

ABKB02000032

ABKB02000022

ABKB02000039

ABKB02000023

PFam32

cp32-like contigs in the B. spielmanii A14S genome

B31 cp32-1

Figure S7

14S contigs that encode PFam32 proteins (green horizontal lines)

ABKB02000022 N-term 186 AA of cp32-12 type PFam32 proteinABKB02000021 C-term 128 C-term cp32-12 type PFam32 proteinABKB02000037 C-term 37 AA of probable cp32-10 PFam32 type protein (best match to lp32-10)ABKB02000031 whole cp32-5 type PFam32 proteinABKB02000026 whole cp32-3 type PFam32 protein

ABKB02000018

ABKB02000035

page 30

1K 2K 3K 4K 5K 6K 7K 8K 9K 10K 11K 12K 13K 14K 15K 16K 17K 18K 19K 20K 21K 22K 23K 24K 25K 26K 27K 28K 29K 30K

3>2>1><1<2<3

Partition genes variable region #2

Rearrangements in cp32-like plasmids in NBu-Bbsl genomes

B31 cp32-1

Figure S8

SV1 cp32-4

Putative phage virion assembly genesRev/Bdr/Mlp genesvariable region #1

Erp/Bap genesvariable region #3/4

MN14-1420 & -1539 cp32-6

MN14-1420 & -1539 cp32-13

PKo cp32-7

PBr cp32-10

PBr cp32-5

VS116 cp32-5

VS116 cp32-7

~10.5 kbp insertion

SV1 cp32-11

~7.4 kbp insertion

site of integration into lp54

~3 kbp indel

* short deletion truncates BGAPBR_V0033, the PFam49 gene in the partition gene cluster

*

Ancient tandem triplication that formed the PFam148 genes

94a lp56-lke

B31 lp38 and VS116 lp17-like

SV1 lp28-4-lke

page 31

5K 10K 15K 20K 25K 30K 35K 40K 45K 50K 55K 60K 65K

5K

10K

15K

20K

25K

30K

3>2>1><1<2<3

DN127 quad

DN

127 cp32-7

Inverted for this compariosn

3>2>1><1<2<3

Partition genes

erp genesDN12

7 qua

d PFa

m32B (c

p32-1

2 trun

cated

)

DN127 q

uad P

Fam32

C (cp3

2-13)

DN127 q

uad P

Fam32

D (cp3

2-12)

DN127 q

uad P

Fam32

A (cp

32-9)

Figure S9

page 32

5000 10K 15K 20K 25K 30K 35K 40K 45K 50K

5000

10K

15K

20K

25K

30K

35K

40K

45K

50K

55K

60K

65K

70K

75K

80K

Scan window = 17/23

B31 lp54

SV

1 lp

54

A75

A20

A35

A50

A46

A52

A41

A53

A56

A33

A34

A32

A57

A40

A54

A48

A49

A55

A38

A47

A39

A45

A43

A37

A42

A44

A36

A51

A69

A68

A64

A73

A62

A76

A60

A61

A70

A65

A71

A74

A66

A67

A59

A63

A23

A25

A06

A02

A03

A15

A24

A05

A11

A10

A16

A14

A30

A31

A08

A12

A07

A04

A19

A21

A22

A01

A18

A28

A26

A09

A13

A58

A72

A17

Figure S10A

cp32

seq

uenc

e

Figure S10BPutative crossover lp54-cp32 point (^) in B. finlandensis SV1 fusion plasmid

GGTCGTTTAGCTTTTCTG^TATTGTATTGTAGCT lp54 -------|-----|---- |--|----------- CAAAAGCTGTGGCTAATA^TTATAGGAGAAGTTA cp32

page 33

hermsii_HS1_chrmturicatae_BET5EL_Chrm

duttonii_Ly_chrmLepto_ParA

hermisii_HS1_cp6-5miyomotoi_CT13--2396_lp6

crocidurae_Achem_plasmid clone 2B31_lp28-2

N40_lp28-2ACA1_lp28-2SV1_lp28-2PKo_lp28-2K78_lp28-2

hermsii_HS1_lpF27turicatae_BET5EL_lp40L

JD1_lp28-7DN127_lp28-7

PBr_lp28-720047_lp28-7ACA-1_lp28-7

PKo_lp28-7BO23_lp28-7

recurrentis_A1_pL37MN14-1420_cp32-4MN14-1539_cp32-4B31_cp32-4

N40_cp32-4297_cp32-4

DN127_cp32-4SV1_cp32-4

K78_cp32-4ACA-1_cp32-4

miyomotoi_CT13--2396_cp1B31_lp28-1F24

WI91-23_lp28-1JD1_lp28-1297_lp28-1

K78_lp28-9ACA1_lp28-9PBi_lp28-9

Bol26_lp28-9PBr_lp28-9

Far04_lp28-972a_cp32-13118a_cp32-13CA11_cp32-13MN14-1420_cp32-13MN14-1539_cp32-13

DN127_cp32-13duttonii_Ly_pL42

B31_lp21156a_lp21

N40_lp36B31_lp36

MN13-1420_lp36MN13-1539_lp36

29805_lp3620047_lp36PBr_lp36Far04_lp36

VS116_lp36A14S_lp36

B31_lp28-329805_lp28-3

Bol26_lp28-3MN14-1420_lp28-3MN14-1539_lp28-3DN127_lp28-3

PBr_lp28-3ACA-1_lp28-3K78_lp28-3A14S_lp28-3PKo_lp28-3BO23_lp28-3

VS116_lp28-3BB31_lp28-1F13

JD1_lp28-6297_lp28-6

CA11_lp56DN127_lp56

WI91-23_lp56B31_lp56

B31_lp38N40_lp38

WI91-23_lp38JD1_lp38

K78_lp38PKo_lp38

ACA-1_lp38BO23_lp38

A14S_lp38hermsii_HS1_lpB58

turicatae_BET5EL_lp44miyomotoi_CT13--2396_lp41

duttonii_Ly_pL23recurrentis_A1_pL23

B31cp26N40_cp26

JD1_cp26SV1_cp26

MN14-1420_cp26MN14-1539_cp26

DN127_cp26ACA-1_cp26PKo_cp26

Tom3107_cp26K78_cp26

BO23_cp26PBr_cp2620047_cp26

Far04_cp26PBi_cp26

A14S_cp26ATCC51557_cp26

VS116_cp26Tom4006_cp26

VA1_cp26hermsii_HS1_lpN31miyomotoi_CT13--2396_lp26recurrentis_A1_pL53

N40_cp32-9JD1_cp32-9B31_cp32-9

297_cp32-9DN127_cp32-9

K78_cp32-9PKo_cp32-9

hermsii_HS1_lpE27297_lp28-5JD1_lp28-5

N40_lp28-5miyomotoi_CT13--2396_lp23

duttonii_Ly_pL41MN14-1420_lp25MN14-1530_lp25

B31_lp25DN127_lp25JD1_lp25

VS116_lp25ATCC51557_lp25

PBr_lp25Far04_lp25

duttonii_Ly_pL28bduttonii_Ly_pL32recurrentis_A1_pL33

miyomotoi_CT13--2396_cp2PKo_lp32-10ACA1_lp32-10PBr_cp32-10

Far04_lp32-10VS116_cp32-10

B31_cp32-10JD1_cp32-10N40_cp32-10

297_cp32-12JD1_cp32-12

DN127_cp32-12quadSV1_lp32-12N40_cp32-12

PKo_cp32-12B31_cp32-8

JD1_cp32-8hermsii_HS1_lpT28

Mayonii1539_cp9Mayonii1420_cp9

DN127_cp9BO23_cp9A14S_cp9

VS116_cp9B31_cp32-1297_cp32-1

MN14-1420_cp32-1MN14-1539_cp32-1

PKo_cp32-1ACA1_cp32-1

duttonii_Ly_pL70recuuentis_A1_pL53

duttonii_Ly_pL26recurrentis_A1_pL35

hermsii_HS1_cp28JD1_cp32-6B31_cp32-6

SV1_lp32-6DN127_cp32-6

MN14-1420_cp32-6MN14-1539_cp32-6

turicatae_BET5EL_lp48duttonii_Ly_pL35

duttonii_Ly_pL36turicatae_BET5EL_lp30

duttonii_Ly_pL27118a_lp32-372a_lp32-3B31_cp32-3MN14-1420_cp32-3MN14-1539_cp32-3297_cp32-3

K78_cp32-3ACA1_cp32-3PKo_cp32-3

SV1_cp32-3A14S_cp32-3

DN127_cp32-3CA-11_cp32-3

JD1_cp32-11297_cp32-11

PKo_cp32-11DN127_cp32-11

SV1_cp32-11 N40_lp28-4B31_lp28-4WI91-23_lp28-4SV1_lp28-4

MN14-1420_lp28-4MN14-1539_lp28-4

DN127_lp28-4PBr_lp28-4

A14S_lp28-4PKo_lp28-4K78_lp28-4ACA1_lp28-4BO23_lp28-4

miyomotoi_CT13-2396_cp394a_lp28-8VS116_lp28-8

A14S_lp28-8PKo_lp28-8K78

BO23_lp28-8ATCC51557_lp28-8

MN14-1420_lp28-10MN14-1539_lp28-10

duttonii_Ly_pL28duttonii_Ly__pL40

B31_cp32-5JD1_cp32-5_+1_

DN127_cp32-5VS116_cp32-5

PBr_cp32-5PKo_cp32-5ACA1_cp32-5

K78_cp32-5A14S_cp32-5

duttonii_Ly_pL31B31_cp32-7N40_cp32-7SV1_cp32-7DN127_cp32-7

PKo_cp32-7VS116_cp32-7

duttonii_Ly_pL15turicatae_BET5EL_lp31

hermsii_megaplasmid_HS1turicatae_BET5EL_lp159

duttonii_Ly_pL165cocidurae _Achema_plasmid clone 1

miyomotoi_CT13-2396_lp72VA1_lp54

ATCC51557_lp54MN14-1420_lp54MN14-1539_lp54

DN127_lp54B31_lp54297_lp54JD1_lp54N40_lp54

SV1_lp54Far04_lp54BPr_lp54

20047_lp54BgVir_lp54

PBi_lp54Tom4006_lp54VS116_lp54

A14S_lp54ACA1_lp54Tom3107_lp54PKo_lp54BO23_lp54K78_lp54

MN14-1420_lp17MN14-1539_lp17K78_lp17A14S_lp1720047_lp17

PBi__lp17VS116_lp17

B31_lp17N40_lp17

0.1

10001000

1000

1000

1000

992

1000

9791000

990

1000

10001000

993

1000

10001000

1000

996

1000

989

999

986

1000

1000

1000

1000

Figure S11

1000

997

999

100010001000

lp21

lp56

lp28-1

lp28-6

lp17

lp28-7

cp32-4

lp28-2

cp32-13

cp26

cp32-3

lp28-9

lp28-8

cp32-10

cp32-5

cp32-6

lp25

lp28-5cp32-9

lp54

cp9cp32-1

cp32-7

lp28-3

cp32-11

lp28-4

lp38

cp32-12

HO14_SAMN02983004_01117PKo_BAPKO_2556

lp36

cp32-8

page 34

supplementary material table of contents10.1186...additional file 1 casjens et al. 1 supplementary...

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