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Structurally divergent and recurrently mutated regions of primate genomes.
Mao, Yafei; Harvey, William T; Porubsky, David; Munson, Katherine M; Hoekzema, Kendra; Lewis, Alexandra P; Audano, Peter A; Rozanski, Allison; Yang, Xiangyu; Zhang, Shilong; Yoo, DongAhn; Gordon, David S; Fair, Tyler; Wei, Xiaoxi; Logsdon, Glennis A; Haukness, Marina; Dishuck, Philip C; Jeong, Hyeonsoo; Del Rosario, Ricardo; Bauer, Vanessa L; Fattor, Will T; Wilkerson, Gregory K; Mao, Yuxiang; Shi, Yongyong; Sun, Qiang; Lu, Qing; Paten, Benedict; Bakken, Trygve E; Pollen, Alex A; Feng, Guoping; Sawyer, Sara L; Warren, Wesley C; Carbone, Lucia; Eichler, Evan E.
Afiliação
  • Mao Y; Department 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.
  • Harvey WT; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Porubsky D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Munson KM; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Hoekzema K; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Lewis AP; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Audano PA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Rozanski A; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Yang X; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
  • Zhang S; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
  • Yoo D; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Gordon DS; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
  • Fair T; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
  • Wei X; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
  • Logsdon GA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Haukness M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Dishuck PC; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Jeong H; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
  • Del Rosario R; McGovern 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.
  • Bauer VL; BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA.
  • Fattor WT; BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA.
  • Wilkerson GK; Department 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.
  • Mao Y; 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.
  • Shi Y; Bio-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 Technol
  • Sun Q; 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.
  • Lu Q; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
  • Paten B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Bakken TE; Allen Institute for Brain Science, Seattle, WA, USA.
  • Pollen AA; Eli 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.
  • Feng G; McGovern 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.
  • Sawyer SL; BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA.
  • Warren WC; Department 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.
  • Carbone L; Department 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;
  • Eichler EE; Department 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.
Cell ; 187(6): 1547-1562.e13, 2024 Mar 14.
Article em En | MEDLINE | ID: mdl-38428424
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Primatas / Genoma Limite: Animals / Humans Idioma: En Revista: Cell Ano de publicação: 2024 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Primatas / Genoma Limite: Animals / Humans Idioma: En Revista: Cell Ano de publicação: 2024 Tipo de documento: Article