ArticleScience (New York, N.Y.)2018
High-resolution comparative analysis of great ape genomes.
Abstract readComparative Study
In one paragraph
Article in Science (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 228 papers.
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228citing papers in PubMed
–field-weighted citation impact
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Who cites it
228 citing papers in PubMed.
- Genomic structural variations distinguishing archaic and modern humans are associated with neurodevelopment.iScience · 2026Article
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Developmental signaling reveals functionally enriched human-specific gene regulation in telencephalic progenitors.bioRxiv : the preprint server for biology · 2026Article
- CellBouncer, a unified toolkit for single-cell demultiplexing and ambient RNA analysis, reveals hominid mitochondrial incompatibilities.Cell genomics · 2026Article
- Tandem repeat variation within and between species reveals signatures of selection in humans and chimpanzees.bioRxiv : the preprint server for biology · 2026Article
- Charting the human-specific properties of gene expression networks in the infant prefrontal cortex.Science advances · 2026Article
- GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.PLoS computational biology · 2026Article
- Article
- Genomic approaches for understanding the evolution of the human brain.Nature neuroscience · 2026Review
- Cross-species prediction reveals chromatin regions with increased accessibility in humans.Science advances · 2026Article
- Species-specific chromatin architecture and neurogenesis mediated by a human enhancer.Cell stem cell · 2026Article
- Article
- Assessing the Potential of Ancient Protein Sequences in the Study of Hominid Evolution.Genome biology and evolution · 2026Article
- The jujube pan-TE map identifies transposable element insertions associated with domestication and pericarp development.Horticulture research · 2026Article
- Boundary-associated propagation of a processed pseudogene dissects pre-existing limitations of genome annotation in the T2T era.Mobile DNA · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Trends of laboratory nonhuman primate licensing in China between 2020 and 2024: A national database analysis.PloS one · 2026Article
- Mapping cis- and trans-regulatory target genes of human-specific deletions.Nature communications · 2025Article
- Retroviral insertions contributed to the divergence of human and chimpanzee brains.bioRxiv : the preprint server for biology · 2025Article
- Interrogating the Regulatory Function of HAQERs during Human Cortical Development.bioRxiv : the preprint server for biology · 2025Article
168 more citing papers are in PubMed but not listed here.
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Authors and funding
44 authors.
Zev N KronenbergDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Ian T FiddesUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.ORCID 0000-0002-1580-7443
David GordonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0001-6552-4022
Shwetha MuraliDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Stuart CantsilierisDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Olivia S MeyersonDepartment of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0003-4040-2226
Jason G UnderwoodDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Bradley J NelsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-7739-7996
Mark J P ChaissonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Max L DoughertyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-0841-0675
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0001-8413-6498
Alex R HastieBionano Genomics, San Diego, CA 92121, USA.ORCID 0000-0001-5829-2649
Mark DiekhansUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.ORCID 0000-0002-0430-0989
Fereydoun HormozdiariDepartment of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA.
Nicola LorussoDepartment of Biology, University of Bari, Aldo Moro, Bari 70121, Italy.ORCID 0000-0001-5878-6403
Kendra HoekzemaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Ruolan QiuDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Karen ClarkNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Archana RajaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
AnneMarie E WelchDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Melanie SorensenDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-1525-9707
Carl BakerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Robert S FultonDepartments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Joel ArmstrongUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.ORCID 0000-0003-2077-4671
Tina A Graves-LindsayDepartments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Ahmet M DenliThe Salk Institute for Biological Studies, La Jolla, CA 92037, USA.ORCID 0000-0003-4407-9059
Emma R HoppeDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-8544-9055
PingHsun HsiehDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0001-8294-6227
Christopher M HillDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-6932-6303
Andy Wing Chun PangBionano Genomics, San Diego, CA 92121, USA.ORCID 0000-0002-0558-3802
Joyce LeeBionano Genomics, San Diego, CA 92121, USA.ORCID 0000-0002-3492-1102
Ernest T LamBionano Genomics, San Diego, CA 92121, USA.
Susan K DutcherDepartments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.ORCID 0000-0001-5689-5753
Fred H GageThe Salk Institute for Biological Studies, La Jolla, CA 92037, USA.ORCID 0000-0002-0938-4106
Wesley C WarrenDepartments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.ORCID 0000-0003-2255-2730
Jay ShendureDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.ORCID 0000-0002-1516-1865
David HausslerUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.ORCID 0000-0003-1533-4575
Valerie A SchneiderNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Han CaoBionano Genomics, San Diego, CA 92121, USA.ORCID 0000-0003-3612-6169
Mario VenturaDepartment of Biology, University of Bari, Aldo Moro, Bari 70121, Italy.ORCID 0000-0001-7762-8777
Richard K WilsonDepartments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Alex PollenDepartment of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0003-3263-8634
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. eee@gs.washington.edu.ORCID 0000-0002-8246-4014
Funding
National Biomedical Information ServicesZIHLM200888 · NLM · NATIONAL LIBRARY OF MEDICINE · PI PALTOO, DINA · 2009 to 2025
$5200.7MLarge Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7MUniversity of Washington Medical Scientist Training Program: MD/PhDT32GM007266 · NIGMS · UNIVERSITY OF WASHINGTON · PI HORWITZ, MARSHALL S. · 1985 to 2023
$30.4MGENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MTraining SubprojectU54HG007990 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI HAUSSLER, DAVID H, PATTERSON, DAVID · 2014 to 2018
$14.8MSequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3MImproving the Human Reference Genome ResourceU41HG007635 · NHGRI · WASHINGTON UNIVERSITY · PI WILSON, RICHARD K. · 2014 to 2017
$9.6MImproving detection and interpretation of clinically relevant structural variationU24HG009081 · NHGRI · WASHINGTON UNIVERSITY · PI EICHLER, EVAN, FULTON, ROBERT SCOTT · 2016 to 2018
$6.8MMassively Parallel Contiguity MappingR01HG006283 · NHGRI · UNIVERSITY OF WASHINGTON · PI SHENDURE, JAY ASHOK · 2011 to 2016
$3.4MThe 200 mammals project: sequencing genomes by a novel cost-effective method, yielding a high resolution annotation of the human genome.R01HG008742 · NHGRI · BROAD INSTITUTE, INC. · PI BIRREN, BRUCE W., KARLSSON, ELINOR · 2016 to 2020
$2.8MGene and Protein Annotation in Highly-Identical Segmental DuplictionsF30HG009478 · NHGRI · UNIVERSITY OF WASHINGTON · PI DOUGHERTY, MAX LOGAN · 2017 to 2020
$162kHoward Hughes Medical InstituteNHGRI NIH HHS F30 HG009478NHGRI NIH HHS R01 HG002385NHGRI NIH HHS R01 HG006283NHGRI NIH HHS R01 HG008742NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U24 HG009081NHGRI NIH HHS U41 HG007234NHGRI NIH HHS U41 HG007635NHGRI NIH HHS U54 HG003079NHGRI NIH HHS U54 HG007990NIGMS NIH HHS T32 GM007266
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.
Indexed as
Evolution, MolecularGenome, HumanAnimalsContig MappingGenetic VariationHominidaeHumansMolecular Sequence AnnotationSequence Analysis, DNA
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