Additional file 2. Mapping statistics of input read pairs mapped to the reference genomes. Sequencing reads derived from the Chinese strain SRA data were mapped to the Treponema pallidum subsp. pallidum (TPA) SS14 and Nichols reference genomes [6] and to the rabbit genome (Statistics was calculated from post-processed mappings; repetitive and homologous sequences and PCR duplicated reads were excluded from the statistics)

David Šmajs (48851)

Fernando González-Candelas (41416)

Jan Oppelt (3815176)

Kay Nieselt (27239)

Lenka Mikalová (133591)

Michal Strouhal (48850)

Natasha Arora (118636)

BMC Research Notes

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MOESM2 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

[Objective]: Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identifed. Recently, Sun et al. (Oncotarget 2016. https://doi. org/10.18632/oncotarget.10154) described a new “phylogenetic group” (called Lineage 2) among Chinese TPA strains. This lineage exhibited a “mosaic genomic structure” of Nichols-like and SS14-like lineages.[Results]: We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identifed: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains.This work was supported by grants from the Grant Agency of the Czech Republic to DS and MS (GA17-25455S, GJ17-25589Y), by grant from the Czech Health Research Council to DS (17-31333A), and by funds from the Faculty of Medicine of the Masaryk University to junior researchers LM and MS.Peer reviewe

Strouhal, Michal

Oppelt, Jan

Mikalová, Lenka

Arora, Natasha

Nieselt, Kay

González-Candelas, Fernando

Šmajs, David

Digital.CSIC

Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

Michal Strouhal

Jan Oppelt

Lenka Mikalová

Natasha Arora

Kay Nieselt

Fernando González-Candelas

David Šmajs

Crossref

Abstract Objective Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new “phylogenetic group” (called Lineage 2) among Chinese TPA strains. This lineage exhibited a “mosaic genomic structure” of Nichols-like and SS14-like lineages. Results We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains

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Additional file 3. Genome coverage statistics for individual Chinese strains. Sequencing reads derived from the Chinese strains SRA data were mapped to the TPA SS14 and Nichols reference genomes [6]. The number of bases with a coverage depth of 1 or more, number of bases with more than 10× coverage depth and average/median coverage depth are shown. Statistics were calculated from previously post-processed mappings; repetitive and homologous regions and PCR duplicated reads were excluded from statistical analysis

MOESM3 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

Additional file 1. Data analysis and methods used in the reanalysis of Chinese Treponema pallidum samples

MOESM1 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

Additional file 9. Genomic SNVs used for phylogenetic analysis. List of SNVs used for construction of phylogenetic trees. Only SNVs detected in all analyzed genomes (i.e., positions with the “N” base in any of the compared genomes were not considered) were used in the analysis. Genes tp0433 (arp), tp0470, and tp0897 (tprK) were excluded from analyses. Altogether, 2444 unique SNV positions were identified when the TPE Fribourg-Blanc genome sequence was used as an outgroup. Coordinates (positions) and gene annotations according to the SS14 genome (CP04011.1); “NA” = not annotated (IGR, intergenic region); “.” = deletion

MOESM9 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

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MOESM2 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

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