Figure 5

Examples of large breaks in sequence collinearity in the heterochromatin borders. A. Alignment of RH haplotype {0} MTP 1058 to the DM reference genome. The start of MTP 1058 {0} is missing in DM. The yellow band indicates an unsequenced region in MTP 1058 {0}, estimated to be 80 kb in length. B. Alignment of RH haplotype {1} MTP 1685 to the same section of the DM reference genome. Alignment gaps of 145 kb and 164 kb to DM are found at different positions compared to (A). The position of BAC clone RH048J07 (yellow) is shown in MTP 1685 {1}. This clone was used for in situ hybridization in Figures 1B and 2. C. Alignment of the two RH haplotypes shows two large inserts of 188 kb and approximately 266 kb in MTP 1058 {0}. The position of BAC clone RH048J07 (yellow) is shown in MTP 1685 {1}. This clone was used for in situ hybridization in Figures 1B and 2. D. The terminal 270 kb of RH MTP 3074 {0} from the south arm has no overlap with the DM sequence. The remaining part of MTP 3074 {0} has a very fragmented collinearity with DM, which disappears in the boxed area. This box marks a sequence duplication region that contains - among others - five DNA repair helicase genes. Scale bar 200 kb applies to all figure panels.