Figure S1: Relationship of the finished sequence map to genetic and radiation
hybrid maps of chromosome 15. Red diamonds represent the physical positions of
genetic markers on the sex-averaged DeCode genetic map. Blue diamonds represent
the physical positions of markers on the Whitehead radiation hybrid map.
Figure S2: Segmental duplication structure of human Chromosome 15.
Intrachromosomal duplications are shown as lines connecting the proximal copy
(center bar) to the distal copy. Distal copies are shown above the center line for direct
repeats and below for inverted. Red lines indicate interchromosomal duplications.
Figure S3: Density plot(s) of the proximal element (coverage map). The number of
chromosome 15 duplicons overlapping each base of the 18.89 Mb PWS duplicon is
shown on the vertical axis. The horizontal axis runs along the length of the reference
element (0-215 kb). The inset shows detail of the region identified as LCR15 (~132147 kb in the main figure). The red box within the inset shows the approximate
boundaries of the region chosen as the “core element”, including the highest sustained
coverage peak.
Figure S4: Detailed history of the structural organization of human
Chromosome 15. Compare to Figure 4 in the main text. Black trapezoids indicate
modern centromeres and black ovals modern telomeres (the modern macaque 7
centromere, not depicted, is in 15qC at 80-81 Mb in human). Chromosome segments
are not necessarily to scale. The ancestral primate sequence (not shown) would have
still contained the ancestral inversion of B-C. Although chicken has significant
inversion rearrangement (including the mixing of sequences from adjacent human
chromosome segments), the central portion including the A-C and C-B junctions is
contiguous. The additional breakage of 15qB is chicken-specific and not ancestral.
The mammalian ancestor (not shown) is identical to the boreoeutherian except for the
breakage of 15qA as shown in chicken and confirmed by opossum (not shown).
Opossum also supports the junctions of 15qA-C, 15qB-14, and 15qA-2 as ancestral as
well as the ancestral contiguity of 15qB in all mammals.
Figure S5: Phylogenetic tree of core element with macaque included. Only the
chromosome 2 and 10 orthologs cluster most closely with a single human copy. Other
macaque elements split between the proximal and distal clusters but show duplication
independent of human elements.
Figure S6: Segmental duplication structure of the Prader-Willi/Angelman
syndrome region on proximal Chromosome 15. A 12 Mb region of the 15q11-q13
genome assembly was extracted and subjected to segmental duplication analyses
using the whole-genome alignment comparison (WGAC) and whole-genome shotgun
sequence detection (WSSD) methods. The WSSD track indicates regions duplicated
as a measure of shotgun sequence read depth, the WGAC track displays
interchromosomal (red) and intrachromosomal (blue) segmental duplications based on
a sequence similarity comparison to the entire assembly. Gaps are indicated as gray
boxes above the WGAC and WSSD tracks. Below the three central tracks is a
breakdown of individual duplications detected by the WGAC method on a vertical
scale of sequence identity, and each block represents a segmental duplication colored
as to the chromosome of origin (Chromosome 15 duplications are shown in light
green). Depicted above the central tracks is the relationship of a subset of sequenced
RP11 clones that are not present within the assembly, or remain unanchored to unique
sequence due to duplication-induced gaps. Note the extensive homology to multiple
regions within 15q11-q13, highlighting the extremely complex inter-relatedness of the
15q11-q13 duplication clusters, especially in the PWS/AS breakpoints (indicated as
BP1, BP2 and BP3).