Fig 1.
Physical maps of three fragments of strain LB-2001 Borrelia miyamotoi plasmids lpB, lpD, and lpE that contain sequences for vsp genes (red arrows), vlp genes (blue arrows), and/or plasmid partition and replication genes (green arrows).
Also shown are the locations of other open reading frames (gray arrows), which are indicated by gene names (e.g. guaA and bdr) or by Borrelia burgdorferi open reading frames names (e.g. BBB22) or paralogous family (PF) numbers (e.g. PF50) [35, 36]. When an ORF had no discernible homology with a protein in the GenBank database, it was designated a hypothetical protein (HP). The vsp and vlp genes are further distinguished by an arbitrarily assigned number (e.g. vsp2) and, in the case of vlp genes, by appending their membership in a vlp subfamilies alpha, gamma, and delta with a “A”, “C”, or “D”, respectively. Pseudo genes are indicated by a “Ψ” prefix and yellow arrows. The arrowheads indicate the direction of transcription. The start and stop positions for each open reading frame, the protein translations, and additional annotation are given in the GenBank/EMBL/DDBJ deposits CP010328 (lpB), KR869o94 (lpD), and KU041636 (lpE), respectively. The scale in kilobases (kb) is indicated by the size marker.
Fig 2.
Phylogram of amino acid sequences for four PF32 (ParA) paralogs (red text) of strain LB-2001 B. miyamotoi and corresponding PF32 sequences and their ORF designations (blue text) of strain B31 B. burgdorferi.
The plasmid fragment origin of the PF32 sequence of B. miyamotoi is indicated. The associated plasmids for each of B. burgdorferi sequences are given parentheses. Nodes with bootstrap values of >70% support by neighbor-joining distance criteria from 1000 replicates are indicated. The scale bar represents nucleotide substitutions per site.
Fig 3.
Unrooted distance phylogram with recombination network for codon-aligned partial vsp genes of selected Borrelia species, as implemented by the SplitsTree algorithm.
The sequences were from strain LB-2001 of B. miyamotoi (Bm_LB) from North America, strain FR64 of B. miyamotoi (Bm_FR), strains HS1 and YBT of B. hermsii (Bh_HS1 and Bh_YBT), and strain Oz1 of B. turicatae (Bt_Oz1). The 3 vsp sequences of FR64b were further distinguished by the plasmid fragment contig (e.g. “p36” for “plasmid fragment 36”) they were located on. The sequences in NEXUS format for the alignment are provided in the S1 File. The scale bar indicates the distance.
Fig 4.
Alignments of nucleotide sequences of plasmid fragments lpB and lpD at the 5’ end of the respective vsp1 gene sequences (section A) and downstream of the vsp1 sequences in the region where the two sequences diverge again (section B).
Between these 5’ and 3’ sequences the lpB and lpD were identical. The numbers on the left refer to the positions of accession numbers CP010328 for lpB and KR869o94 for lpD. Differences between the sequences are indicated by gray highlights. An inverted repeat in lpB but not lpD and the 4-base palindromes (TGCA/ACGT) occuring in either sequence are indicated by > and < marks. Consensus ribosome binding sequences and “-10” and “-35” elements of a RpoD-type promoter are indicated by underlining. In section A the translated amino acids for the starts of Vsp1 are shown for both sequences, either above or below the nucleotide sequence. In section B only the first 37 amino acids that was in common to both VlpD1 (lpB) and VlpD5 (lpD) are shown.
Fig 5.
Histogram of numbers of unique RNA-seq reads mapping to different vsp sequences of strains LB-2001 and FR64b of B. miyamotoi, strains HS1 and YBT of B. hermsii, and strain Oz1 of B. turicatae, as well as the flaB sequence of B. miyamotoi.
The sequences are the same as for Fig 3 and are provided in the S1 File. Shuffled versions of the latter sequence and the LB-2001 vsp1 sequence were also included in the set.