Segmental duplications and their variation in a complete human genome | Zendy

Mitchell R. Vollger | Zendy; Xavi Guitart | Zendy; Philip C. Dishuck | Zendy; Ludovica Mercuri | Zendy; William T. Harvey | Zendy; Ariel Gershman | Zendy; Mark Diekhans | Zendy; Arvis Sulovari | Zendy; Katherine M. Munson | Zendy; Alexandra P. Lewis | Zendy; Kendra Hoekzema | Zendy; David Porubský | Zendy; Ruiyang Li | Zendy; Sergey Nurk | Zendy; Sergey Koren | Zendy; Karen H. Miga | Zendy; Adam M. Phillippy | Zendy; Winston Timp | Zendy; Mario Ventura | Zendy; Evan E. Eichler | Zendy

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Segmental duplications and their variation in a complete human genome

Author(s) -

Mitchell R. Vollger,

Xavi Guitart,

Philip C. Dishuck,

Ludovica Mercuri,

William T. Harvey,

Ariel Gershman,

Mark Diekhans,

Arvis Sulovari,

Katherine M. Munson,

Alexandra P. Lewis,

Kendra Hoekzema,

David Porubský,

Ruiyang Li,

Sergey Nurk,

Sergey Koren,

Karen H. Miga,

Adam M. Phillippy,

Winston Timp,

Mario Ventura,

Evan E. Eichler

Publication year - 2022

Publication title -

science

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 12.556

H-Index - 1186

eISSN - 1095-9203

pISSN - 0036-8075

DOI - 10.1126/science.abj6965

Subject(s) - human genome , structural variation , genome , telomere , segmental duplication , biology , sequence (biology) , genetics , computational biology , human disease , reference genome , gene , gene family

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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