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Fig. 2 | Genome Biology

Fig. 2

From: The birth of a human-specific neural gene by incomplete duplication and gene fusion

Fig. 2

HYDIN copy number diversity in humans and great apes. a Diploid aggregate copy number for HYDIN loci based on genome sequencing data from 1KG (611 Africans, 285 admixed Americans, 400 East Asians, 376 Europeans, 451 South Asians), as well as archaic genomes and great apes (14 bonobos, 23 chimpanzees, 32 gorillas, 17 orangutans). Copy number was estimated using average sequence read depth across the 364 kbp segmental duplication as described previously and represents the aggregate diploid copy number for HYDIN and HYDIN2. b FISH analysis of metaphase and interphase chromosomal preparations from four human outliers (enumerated in panel (a)) and one control (aggregate cn = 4 copies) confirms rare duplications (aggregate cn = 5 copies) and losses (aggregate cn = 3 copies) of HYDIN restricted to HYDIN2 on chromosome 1q21.1. c MIP-based genotyping of paralog-specific copy number identifies partial duplications (top and bottom left panels), deletions (top right panel), and putative interlocus gene conversion events (bottom right panel). Each point estimates paralog-specific copy number (red, HYDIN; blue, HYDIN2) based on sequencing read depth over SUNs that distinguish HYDIN paralogs. A total of 153 MIPs were used for genotyping and events were detected by an automated caller. Also shown is the canonical HYDIN gene model (bottom of each plot). d Summary of HYDIN internal structural variation and interlocus gene conversion events based on MIP genotyping of 6055 humans. Duplications (up arrows), deletions (down arrows), and the sole interlocus gene conversion event (horizontal arrow) are colored according to locus (red, HYDIN; blue, HYDIN2) and their spatial extent shown with respect to exonic structure (bottom of plot)

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