ArticleCell2024
Structurally divergent and recurrently mutated regions of primate genomes.
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Article in Cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53citing papers in PubMed
15.2field-weighted citation impact, top 1% of its field
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53 citing papers in PubMed, 67 citations in OpenAlex.
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Corrections and comments
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Authors and funding
34 authors at 14 institutions in 3 countries.
Yafei MaoDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China. Electronic address: yafmao@sjtu.edu.cn.
William T HarveyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
David PorubskyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Kendra HoekzemaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Alexandra P LewisDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Peter A AudanoDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Allison RozanskiDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Xiangyu YangBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
Shilong ZhangBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
DongAhn YooDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
David S GordonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Tyler FairEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Xiaoxi WeiBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
Glennis A LogsdonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Marina HauknessUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Philip C DishuckDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Hyeonsoo JeongDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Ricardo Del RosarioMcGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Vanessa L BauerBioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA.
Will T FattorBioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA.
Gregory K WilkersonDepartment of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA; Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA.
Yuxiang MaoInstitute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
Yongyong ShiBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
Qiang SunInstitute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
Qing LuBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Trygve E BakkenAllen Institute for Brain Science, Seattle, WA, USA.
Alex A PollenEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
Guoping FengMcGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Sara L SawyerBioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA.
Wesley C WarrenDepartment of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA.
Lucia CarboneDepartment of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA.
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. Electronic address: eee@gs.washington.edu.
University of Washington · USShanghai Jiao Tong University · CNHoward Hughes Medical Institute · USUniversity of California, Santa Cruz · USBroad Institute · USMcGovern Institute for Brain Research · USUniversity of California, San Francisco · USUniversity of Colorado Boulder · USAllen Institute for Brain Science · USChinese Academy of Sciences · CNNorth Carolina State University · USOregon Health & Science University · USOregon National Primate Research Center · USThe University of Texas MD Anderson Cancer Center · US
Funding
Upgrade of confocal microscopy at the Oregon National Primate Research CenterP51OD011092 · OD · OREGON HEALTH & SCIENCE UNIVERSITY · PI Bonnie J. Nagel · 2012 to 2026
$203.9MThe WashU-UCSC-EBI Human Genome Reference Center."U41HG010972 · NHGRI · WASHINGTON UNIVERSITY · PI Ira M Hall, Heng Li · 2019 to 2026
$24.9MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MSequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3MDockstore: The Community Platform for Reproducible Biomedical Workflows and ApplicationsU24HG011853 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Jonathan Lawson, Benedict Paten · 2021 to 2026
$5.7MBreaking the Barrier to an HIV VaccineDP1AI175471 · NIAID · UNIVERSITY OF COLORADO · PI Sara Sawyer · 2022 to 2026
$5.5MSequence-resolved structural variation of human genomesR01HG010169 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2018 to 2026
$4.5MHunting the HIV-1 UnicornDP1DA046108 · NIDA · UNIVERSITY OF COLORADO · PI SAWYER, SARA · 2018 to 2022
$4.5MCharacterizing Host-Virus Interactions in a New HIV Model OrganismR01OD034046 · OD · UNIVERSITY OF COLORADO · PI Sara Sawyer · 2022 to 2026
$3.6MThe construction and utility of reference pan-genome graphsU01HG010961 · NHGRI · DANA-FARBER CANCER INST · PI LI, HENG, PATEN, BENEDICT · 2020 to 2023
$3.2MComparative and functional analysis of conservation and rearrangement of topologically associating domains across mammals.R01HG010333 · NHGRI · OREGON HEALTH & SCIENCE UNIVERSITY · PI CARBONE, LUCIA · 2018 to 2021
$2.8MEnabling Comparative PangenomicsR01HG010485 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI HAUSSLER, DAVID H, MARTIN, FERGAL JAMES · 2020 to 2023
$2.6MNHGRI NIH HHS R01 HG002385NHGRI NIH HHS R01 HG010169NHGRI NIH HHS R01 HG010333NHGRI NIH HHS R01 HG010485NHGRI NIH HHS U01 HG010961NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U24 HG011853NHGRI NIH HHS U41 HG010972NIAID NIH HHS DP1 AI175471NIAID NIH HHS R01 AI137011NIDA NIH HHS DP1 DA046108NIGMS NIH HHS K99 GM147352NIGMS NIH HHS R00 GM147352NIH HHS P51 OD011092NIH HHS R01 OD034046
Abstract
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.
Indexed as
GenomePrimatesAnimalsBase SequenceBiological EvolutionGenomic Structural VariationHumansSequence Analysis, DNAadaptive evolutioncomparative genomicsduplicated genesevolutionary medicinehuman diseaseslong-read sequencingNPHP1 and Joubert syndromeprimate evolutionRGPD gene family
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