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Science. 2018 Jun 8;360(6393). pii: eaar6343. doi: 10.1126/science.aar6343.

High-resolution comparative analysis of great ape genomes.

Author information

1
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
2
UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
3
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
4
Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA.
5
Pacific Biosciences (PacBio) of California, Inc., Menlo Park, CA 94025, USA.
6
Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA.
7
Bionano Genomics, San Diego, CA 92121, USA.
8
Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA.
9
Department of Biology, University of Bari, Aldo Moro, Bari 70121, Italy.
10
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
11
Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
12
The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
13
Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
14
Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
15
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. eee@gs.washington.edu.

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.

PMID:
29880660
PMCID:
PMC6178954
DOI:
10.1126/science.aar6343
[Indexed for MEDLINE]
Free PMC Article

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