학술논문
High-resolution comparative analysis of great ape genomes
Document Type
article
Author
Kronenberg, Zev N; Fiddes, Ian T; Gordon, David; Murali, Shwetha; Cantsilieris, Stuart; Meyerson, Olivia S; Underwood, Jason G; Nelson, Bradley J; Chaisson, Mark JP; Dougherty, Max L; Munson, Katherine M; Hastie, Alex R; Diekhans, Mark; Hormozdiari, Fereydoun; Lorusso, Nicola; Hoekzema, Kendra; Qiu, Ruolan; Clark, Karen; Raja, Archana; Welch, AnneMarie E; Sorensen, Melanie; Baker, Carl; Fulton, Robert S; Armstrong, Joel; Graves-Lindsay, Tina A; Denli, Ahmet M; Hoppe, Emma R; Hsieh, PingHsun; Hill, Christopher M; Pang, Andy Wing Chun; Lee, Joyce; Lam, Ernest T; Dutcher, Susan K; Gage, Fred H; Warren, Wesley C; Shendure, Jay; Haussler, David; Schneider, Valerie A; Cao, Han; Ventura, Mario; Wilson, Richard K; Paten, Benedict; Pollen, Alex; Eichler, Evan E
Source
Science. 360(6393)
Subject
Language
Abstract
Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.