Human-Specific Changes of Genome Structure Detected by Genomic Triangulation
R. A. Harris1,2,
J. Rogers3 and
A. Milosavljevic1,2*
1 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
2 Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
3 Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245, USA.
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Fig. 1. Detection by genomic triangulation of a human-specific breakpoint induced by an insertion. In the example shown (left), blockset construction revealed one long conserved block for a chimp-rhesus comparison. However, blocks from human-chimp and human-rhesus blocksets align except for a gap, which suggests that there has been a human-specific insertion. This is further illustrated by the pairwise gapsets. Pairwise blocksets and gapsets between extant species are represented by primary colors (red, blue, and yellow) and those between an extant species and the ancestor are represented by complementary colors (purple, green, and orange). Gapsets are represented as gap maps, with white circles representing gaps and circle coordinates indicating sizes of the gaps in specific genomes. Gapsets on the left indicate breakpoints in human-chimp and human-rhesus pairwise comparisons due to the human breakpoint. Ancestral gapsets on the right indicate the breakpoint between human and the ancestor.
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Fig. 2. Human-specific breakpoints. (A) Chromosome ideograms of 130 human-specific break-points detected by genomic triangulation, with breakpoint counts by chromosome. (B) Gap map with ancestor gap lengths on the x axis and human gap lengths on the y axis. Only gaps greater than 10 kb in at least one of the genomes and smaller than 4 Mb were considered. Some insertions occur to the right of the y = x axis because visual inspection revealed inaccuracies in gap sizing, providing evidence for human insertion. (C) Size distribution of detected human-specific insertions. The percent identity of segmental duplications can indicate the approximate age of duplication events.
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