Treponema pallidum subsp. pallidum has a single, circular chromosome with a size of approximately 900 kilobase pairs.

The genome size and chromosome conformation of Treponema pallidum subsp. pallidum, Nichols strain, were determined by contour-clamped homogeneous electric field electrophoresis, a pulsed-field gel electrophoresis technique. Digestion of T. pallidum subsp. pallidum DNA with the restriction endonucleases NotI and SpeI produced 12 and 26 fragments, respectively. Summation of the physical lengths of the fragments produced by NotI and SpeI cleavage yielded average sizes of 900 and 913 kbp, respectively, for the genome of T. pallidum subsp. pallidum. Contour-clamped homogeneous electric field electrophoresis of T. pallidum subsp. pallidum DNA exposed to 4 krads of gamma irradiation resolved a single band of 800 to 1,000 kbp; treatment of the DNA with 16 krads of gamma irradiation resulted in the production of smaller fragments, whereas untreated DNA did not migrate into the gels. The gamma irradiation results indicate that T. pallidum subsp. pallidum has a single, circular chromosome that was linearized at a dosage of 4 krads of gamma irradiation. The size estimate provided by restriction endonuclease digestion with NotI and SpeI shows that the genome of T. pallidum subsp. pallidum, at approximately 900 kbp, is considerably smaller than the 13,700-kbp genome size calculated from renaturation kinetics.