Recurrent duplication-driven transposition of DNA during hominoid evolution

Johnson et al. 10.1073/pnas.0605426103.

Supporting Information

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Supporting Table 4
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Supporting Figure 4

Fig. 4. Map locations of primate LCR16a. Map location of LCR16a based on BAC-end sequence analysis. Map locations are shown against a human chromosomal ideogram. Arrows show the direction of transcription with respect to the morpheus gene model for the LCR16a duplication; + denotes ancestral locus positions in baboon, and * identifies lineage-specific insertions.

Supporting Figure 5

Fig. 5. Sequence alignment of LCR16a loci. Nonhuman primate genomic sequence and corresponding segment in the human genome are compared (see Fig. 2 for a more detailed description). In addition to the WSSD tracks, the estimated copy number of each region is indicated based on the corresponding number of reads per 5 kb.

Supporting Figure 6

Fig. 6. The duplication architecture of primate loci is shown in the context of a neighbor-joining (NJ) phylogenetic tree for LCR16a (2-kb noncoding sequence). Loci encoded by species [HSA (Homo sapiens), PTR (Pan troglodytes), GGO (Gorilla gorilla), PPY (Pongo pygmaeus), and PHA (Papio hamadryas)] and relative to human orthologous loci (Fig. 1). New insertions or ambiguous loci were given a letter designation.

Supporting Figure 7

Fig. 7. Copy-number and sequence divergence flanking LCR16a in orangutan (a) and human (b). Orangutan genomic sequence AC145295 was analyzed by WSSD analysis against orangutan whole-genome sequencing (WGS) and shown to be completely duplicated (blue bar, >94%). Approximate copy number (orange) and average degree of sequence identity (above the line) were estimated. Both copy number and divergence decrease in a gradient-like fashion from LCR16a, which is the only corresponding segment duplicated in human (pink) and chimpanzee (light blue). A virtually identical analysis using an ≈185-kb segment from human chromosome 16 against human WGS shows the segment to be duplicated in chimpanzee and human in a gradient-like fashion. The only duplicated segment in orangutan (blue bar) corresponds to the LCR16a segment.

Supporting Figure 8

Fig. 8. Phylogeny of LCR16 loci. NJ trees with corresponding bootstrap support (n = 1,000 replicates) for each of the LCR16 duplicons.

Supporting Figure 9

Fig. 9. More diverged LCR16a loci on chromosomes 11, 10, and X. (a) NJ phylogeny with respect to human and baboon copies. (b) The extent of genomic-sequence overlap with LCR16a consensus based on BLAST sequence similarity. NPIP, nuclear pore-interacting protein human mRNA. DogChr.6 represents the extent of BLAST sequence homology (>70%) from dog chromosome 6 (July, 2004) to this locus. This particular region of dog chromosome 6 is syntenic to human chromosome 16.

Supporting Figure 10

Fig. 10. Sequence resolution of breakpoint structures. Shown is a schematic of repeat content and optimal global alignment at the breakpoints between human and nonhuman primate new insertions.