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Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution

Figure 6

PCR analysis of human-specific and chimpanzee-specific RD.

(A–D) PCR genotyping of the human-specific RD at chr15:31,987,740–31,988,005 in the 2006 hg18 assembly. For all 20 European (A) and 20 South American (B) individuals surveyed, the size of the PCR products is consistent with the homozygous presence of the acceptor sequence in all individuals tested. In contrast, among 20 African-American (C) and 20 Asian individuals (D) surveyed, several DNA samples yielded PCR products consistent with the absence of the acceptor sequence, either as homozygous [lanes 4–6 in (C) and 4, 9, and 10 in (D)] or heterozygous [lanes 3, 11, and 13 in (C) and 5, 7, and 8 in (D)]. See Table S2 for full loading orders. (E) Example of PCR validation of human-specific RD (chr10: 96,228,347–96,228,586): PCR products of size consistent with the presence of the acceptor sequence were obtained in human DNA (from HeLa cells or pooled individuals [Pop80]), while shorter PCR products, indicative of the absence of the acceptor sequence, were obtained with chimpanzee, gorilla, and orangutan DNA. (F) Example of PCR validation of chimpanzee-specific RD (chr7:136,854,307–136,854,636): PCR products of size consistent with the presence of the acceptor sequence were obtained with chimpanzee DNA (from single, “chimpanzee,” or pooled individuals [Pop12]), while shorter PCR products, indicative of the absence of the acceptor sequence, were obtained with human (HeLa cells), gorilla, and orangutan DNA.

Figure 6

doi: https://doi.org/10.1371/journal.pgen.1000469.g006