6533b828fe1ef96bd1287b8f

RESEARCH PRODUCT

MOESM7 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

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Additional file 7. Alignment of tprD/tprD2 alleles. tprD and tprD2 alleles were downloaded from the NCBI GenBank database for each reference Nichols and SS14 TPA strain, CP004010.2 and CP004011.1 [6], respectively. While the Nichols reference genome harbors identical copies of tprC and tprD genes, the SS14 reference genome carries the tprD2 allele, which is not identical to the tprC gene and differs from the tprD allele by roughly 320 nucleotides. As shown in the alignment, we were able to identify the tprD2 allele (in positions 800–1791 according to the SS14 tprD2 allele) among the sequencing reads from the Chinese SRA data. The alignment was performed using SeqMan software (DNASTAR, Madison, WI, USA).