Additional file 1: of Primordial origin and diversification of plasmids in Lyme disease agent bacteria

Figure S1. Borreliella plasmid PFam32 protein neighbor-joining tree. Figure S2. Two examples of Borreliella linear plasmids with low protein coding potential. Figure S3. Comparative maps of linear plasmids in Borreliella isolates. Maps of the following linear plasmids are shown in the following panels: A, lp5; B, lp17; C, lp25; D, lp28–2, lp28–6, lp28–7 and lp28–9; E, lp28–3; F, VS116 lp28–3; G, lp28–4; H, lp28–8; I, lp32; J, lp36; K, lp38; L, lp56. Figure S4. The PFam54 gene cluster of the Borreliella lp54 plasmids. Figure S5. Ends of the Borreliella linear chromosome sequences. Figure S6. Comparative maps of cp9 plasmids in Borreliella isolates. Figure S7. Orphan cp32-like contigs in the B. spielmanii A14S genome. Figure S8. Rearrangements in cp32-like plasmids in NBu-Borreliella genomes. Figure S9. B. bissettiae DN127 66 kbp circular plasmid cp32-quad. Figure S10. B. finlandensis SV1 integration of cp32 into lp54. Figure S11. Borreliella and relapsing fever Borrelia PFam32 neighbor-joining tree. Table S1. Borreliella and relapsing fever Borrelia PFam32. (PDF 6030 kb

Additional file 1: Figure S1. of Plasmid diversity and phylogenetic consistency in the Lyme disease agent Borrelia burgdorferi

B. burgdorferi plasmid PFam32 protein tree. Figure S2. Comparative maps of linear plasmids in 14 B. burgdorferi isolates. Maps of the following linear plasmids are shown in the following panels: A, lp5; B, lp17; C, lp21; D, lp25; E, lp28-1; F, lp28-2, lp28-6, lp28-7 and lp28-9; G, lp28-3; H, lp28-4; I, lp28-5; J, lp28-6; K, lp32-3; L, lp36; M, lp38; N, lp54; O, lp56. Figure S3. Deletions in cp32 circular plasmids. Figure S4. Comparative cp9 plasmid maps. Figure S5. All possible recombination products. Figure S6. Ancestral transfer of genetic material from the B. burgdorferi chromosome right end to a linear plasmid. Table S1. Linear plasmid locations of selected genes. (PDF 3869 kb

Additional file 1 of A high fidelity approach to assembling the complex Borrelia genome

Additional file 1: Table S1. QUAST and Merqury results. Table S2. Detailed information about assembly results after genome reconstruction of PBaeII, PBes and 89B13. Table S3. Summary of mapping statistics of PBaeII. Table S4. Mapping statistics for single genome elements of PBaeII. Table S5. List and characteristics of all isolates. Figures S1-S3. Dot plots B. bavariensis PBaeII. Figure S4. Dot plots B. garinii PBes, lp32-10, microbial assembler. Figure S5. Dot plot B. valaisiana 89B13, lp32-7, IPA. Figure S6. Dot plot B. valaisiana 89B13, lp25, microbial_circulomics. Figure S7. Mapping graphs of B. bavariensis PBaeII