FIG. 1.

CGH data for 137 B. pertussis strains, arranged by collection. Abbreviations: lab, laboratory strains; pre-, prevaccine era (1935 to 1958); post-, postvaccine era (1977 to 2005); Cinn. 1993, from a 1993 outbreak in Cinncinati, Ohio; Cinn. other, from Cinncinati between 1989 and 1994 but not during the 1993 outbreak; unvacc., unvaccinated patients; vacc., vaccinated patients. Each column represents a strain; each row represents a microarray element (usually the average of duplicates), arranged in Tohama I genome order from the top of the figure to the yellow bar. The dagger designates Tohama I; the asterisk designates strain 18323 (both in the lab strains collection). Arrowheads indicate RDs, defined as two or more adjacent genes not detected in three or more strains. RDs consisting of prophage genes are marked with φ next to the number. Yellow bar, genes duplicated in Tohama I. Magenta bar, genes not present in the Tohama I sequence, arranged in B. bronchiseptica RB50 order. Missing data are gray (display excludes genes with missing data from more than 25% of arrays).