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Segmental duplications and their variation in a complete human genome. 2022
Mitchell R Vollger, and
Xavi Guitart, and
Philip C Dishuck, and
Ludovica Mercuri, and
William T Harvey, and
Ariel Gershman, and
Mark Diekhans, and
Arvis Sulovari, and
Katherine M Munson, and
Alexandra P Lewis, and
Kendra Hoekzema, and
David Porubsky, and
Ruiyang Li, and
Sergey Nurk, and
Sergey Koren, and
Karen H Miga, and
Adam M Phillippy, and
Winston Timp, and
Mario Ventura, and
Evan E Eichler
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Despite their importance in disease and evolution, highly identical segmental duplications (SDs) are among the last regions of the human reference genome (GRCh38) to be fully sequenced. Using a complete telomere-to-telomere human genome (T2T-CHM13), we present a comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence, increasing the genome-wide estimate from 5.4 to 7.0% [218 million base pairs (Mbp)]. An analysis of 268 human genomes shows that 91% of the previously unresolved T2T-CHM13 SD sequence (68.3 Mbp) better represents human copy number variation. Comparing long-read assemblies from human (n = 12) and nonhuman primate (n = 5) genomes, we systematically reconstruct the evolution and structural haplotype diversity of biomedically relevant and duplicated genes. This analysis reveals patterns of structural heterozygosity and evolutionary differences in SD organization between humans and other primates.
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