Figure 3

Synteny of SDs on 22q11.2. (A) The syntenic relationship of the subunits with chimpanzee, orangutan and macaque is shown as present (matching color boxes) or absent (white). This map was derived from our analysis of the multi-genome alignment data in the Ensembl database (see Methods). The boxed region in LCR22-5' was subsequently confirmed by PCR to be absent in the macaque genome (see Additional file 3, Figure S2). (B) Comparison of primate segmental duplications. The data were retrieved from a previous study using WSSD analysis for SD detection [29]. The depth of sequence read coverage (number of shot-gun sequencing reads in 5-kb windows) is depicted for human (HAS), chimpanzee (PTR), orangutan (PPY) and macaque (MMU) based on alignment of reads against the human genome. Putative duplicated regions with excess read depth (more than three standard deviation of the mean) are shown in red with unique regions in green. Human and chimp SDs derived from depth analysis are also shown below the human SDs derived from WGAC analysis (top). The data here suggest that most of the sequences in LCR22-2', -3a' and -4' are shared between human and chimpanzee and their duplications likely occurred after the split of the African great apes from Asian great apes. Interestingly, the human-specific SDs in LCR22-3a' and -4' show higher sequence identity (represented by light to dark orange color) than the rest of the SDs (light to dark grey). (C) Past duplication events that may have generated the homology between LCR22-3a' and LCR22-4'. Arrow lines represent putative duplication directions. The large cyan subunit in LCR22-3a' may have arisen from either the proximal or distal paralogous sequences in LCR22-4'.