(A) Schematic representation of PCR and sequence-based strategies used to further investigate genomic deletion or divergence. Two couples of primers were designed based on the genome sequence of T. whipplei Twist strain, including one (F1/R1) flanking the gene predicted absent/divergent by CGH analysis, and another (sF1/sR1) flanking the PCR amplicon spotted on the microarray represented by the hatched square. (B) PCR analysis of a putative TWT596 deletion on various T. whipplei strains. The amplicon size obtained using the primers TWT595F1 and TWT597R1 and T. whipplei Twist DNA as positive control was of 2040 nt. Lower size amplicons were obtained with Slow2, Endo5, Neuro1, DigADP11, Dig15 and DigNeuro18, indicating that the gene was deleted in these strains. The first lane corresponds to DNA size standard (1 kb DNA ladder, Invitrogen).