FIG. 1.

Schematic representation of large sequence polymorphism Johnin. Coordinates on the genome are given as base pairs starting from the first nucleotide of the start codon of dnaA in M. avium 104 and M. avium subsp. paratuberculosis K10, respectively. White boxes represent homologous sequences across M. avium 104, M. avium subsp. paratuberculosis K10, and M. avium subsp. paratuberculosis strains used to produce Johnin. The striped box represents a large sequence (LSP^p4) that is present in M. avium subsp. paratuberculosis but missing in M. avium 104. LSP^jn is depicted by the gray box and is missing from M. avium subsp. paratuberculosis strains III, IV, C286, C300, III.V, 3+5, and C. Thick arrows represent primers flanking LSP^jn (bridging primers); a PCR product is obtained if the region is missing. Thin arrows represent primers targeting a sequence within LSP^jn; a PCR product is obtained if the sequence is present.