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September 22, 2019  |  

High-resolution comparative analysis of great ape genomes.

Authors: Kronenberg, Zev N and Fiddes, Ian T and Gordon, David and Murali, Shwetha and Cantsilieris, Stuart and Meyerson, Olivia S and Underwood, Jason G and Nelson, Bradley J and Chaisson, Mark J P and Dougherty, Max L and Munson, Katherine M and Hastie, Alex R and Diekhans, Mark and Hormozdiari, Fereydoun and Lorusso, Nicola and Hoekzema, Kendra and Qiu, Ruolan and Clark, Karen and Raja, Archana and Welch, AnneMarie E and Sorensen, Melanie and Baker, Carl and Fulton, Robert S and Armstrong, Joel and Graves-Lindsay, Tina A and Denli, Ahmet M and Hoppe, Emma R and Hsieh, PingHsun and Hill, Christopher M and Pang, Andy Wing Chun and Lee, Joyce and Lam, Ernest T and Dutcher, Susan K and Gage, Fred H and Warren, Wesley C and Shendure, Jay and Haussler, David and Schneider, Valerie A and Cao, Han and Ventura, Mario and Wilson, Richard K and Paten, Benedict and Pollen, Alex and Eichler, Evan E

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. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Journal: Science
DOI: 10.1126/science.aar6343
Year: 2018

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