The 3′ end of A. phagocytophilum virB6-4 genes is composed of an unusually large tandem repeat region, which exhibits dramatic variability among strains.A. Map of the human HZ strain virB6-3 and virB6-4 genes, highlighting the location and structure of several repeat regions (R1-R4). The most variability occurred in R4; this region is 5.88 kb larger than previously reported for the ApHZ genome (CP000235). The original sequence is diagrammed above the map, with the dashed line representing the segment missing in CP000235. Larger repeated R4 segments of 2.7 kb and 1.15 kb are indicated above. Vertical black bars within each gene designate segments encoding predicted transmembrane domains. BamHI sites, of which there is one in all R4 type 2 repeats (see Figure S2B), are indicated. Also shown are the positions of PCR primers used in C. B. BamHI genomic maps depicting the virB6-4 locus (black arrows).The segment encompassing R4 is highlighted below each respective map. In the regions outside the virB6-4 locus, corresponding BamHI fragments are shown in the same color. Overall, the optical map sizes were in good agreement with the actual sizes, except within R4. This is attributed to the limitation of optical mapping in resolving fragments <2 kb. Despite these discrepancies, the cumulative size of the genomic region encompassing virB6-4 in the optical map is in close agreement with that in the ApDog1 genome sequence. C. The variability in size of PCR products spanning virB6-4 repeat regions R4 and R3/R4 in diverse A. phagocytophilum strains.
Al-Khedery et al. BMC Genomics 2012 13:678 doi:10.1186/1471-2164-13-678