Table 2. Frameshift mutations and substitutions resulting in significant protein truncations, elongations and novel annotations in the Bosnia A genome in comparison with TPA and TPE strains.

Gene Predicted protein/Functiona	Nucleotide difference in Bosnia A strain	Difference in comparison with	Identity to	Coordinates of the difference in the Bosnia A genome (CP007548.1)	Result of the frameshift mutation/substitution
TENDBA_0009	2 bp insertionb	TPA strains	TPE strains	9428–9429	reverted frameshift mutation
TprA/Virulence					functional tprA gene
TENDBA_0082a	1 bp insertion	TPA/TPE strains	Bosnia A-specific	92250	frameshift mutation, significant protein truncation
HP/Unknown					gene annotated as pseudogene
TENDBA _0103	1 bp deletion	TPA strains	TPE strains	113544–113545	reverted frameshift mutation
RecQ/DNA replication, repair and recombination					functional recQ gene
TENDBA_0126b	65 bp insertion	TPA strains	TPE strains	149005–149069	frameshift mutation, gene elongation
HP/Unknown	1 bp deletion	TPA/TPE strains	Bosnia A-specific	149363–149364	prediction of TENDBA_0126b genec
TENDBA _0314	1 bp deletion	TPA strains	TPE strains	331583–331584	frameshift mutation
TCHP/Unknown					fusion of genes orthologous to TPA genes TP0314 and TP0315 (813 bp)
TENDBA _0316	635 bp insertion	TPA strains	TPE strains	332334–332968	reverted frameshift mutation, chimeric tprGId
TprGI/Virulence	2300 bp deletion	TPA/TPE strains	Bosnia A-specific	333273–333274	gene annotated as pseudogene
TENDBA_0370	1 bp substitution	TPA strains	TPE strains	394198	internal stop codon generation, significant protein truncation
HP/Unknown					gene annotated as pseudogene
TENDBA _0548a	52 bp insertion	TPA strains	TPE strains	592543–592594	frameshift mutation
HP/Unknown					prediction of TENDBA_0548a genec
TENDBA _0671	1 bp substitution	TPE strains	TPA strains	736075	alternative start codon generation, gene elongation
Ethanolamine-phosphotransferase/General metabolism
TENDBA _0911a	1 bp deletion	TPA strains	TPE strains	989806–989807	frameshift mutation
HP/Unknown					prediction of TENDBA_0911a genec
TENDBA _1029	2 bp deletionb	TPA/TPE strains	Bosnia A-specific	1123143–1123144	frameshift mutation, significant protein truncation
TCHP/Unknown					gene annotated as pseudogene
TENDBA _1031	378 bp insertion	TPE strains	TPA strains	1123623–1124000	frameshift mutation, gene elongationd
TprL/Virulence	(including 1 bp deletion specific for Bosnia Ab)			1123700–1123701

^aHP – hypothetical protein, TCHP – treponemal conserved hypothetical protein.

^bnucleotide differences in the regions containing simple sequence repeats (short tandem repeats); when compared, tprA gene was functional in Bosnia A and TPE strains and not among TPA strains (except for strain Sea 81-4; see [37]).

^cdue to same nucleotide differences (indels), orthologous genes to TENDBA_0126b, TENDBA_0548a and TENDBA_0911a genes were previously predicted in all TPE strains when compared to the TPA genomes.

^d [27].