Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.

Autor: Warren WC; Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. warrenwc@missouri.edu jr13@bcm.edu eee@gs.washington.edu.; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65211, USA.; Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA., Harris RA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Haukness M; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Fiddes IT; Inscripta Inc., Boulder, CO 80301, USA., Murali SC; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA., Fernandes J; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Dishuck PC; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Storer JM; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.; Institue for Systems Biology, Seattle, WA 98109, USA., Raveendran M; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Hillier LW; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Porubsky D; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Mao Y; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Gordon D; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA., Vollger MR; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Lewis AP; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Munson KM; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., DeVogelaere E; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Armstrong J; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Diekhans M; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Walker JA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA., Tomlinson C; McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA., Graves-Lindsay TA; McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA., Kremitzki M; McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA., Salama SR; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Audano PA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Escalona M; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Maurer NW; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Antonacci F; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy., Mercuri L; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy., Maggiolini FAM; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy., Catacchio CR; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy., Underwood JG; Pacific Biosciences of California, Seattle, WA 94025, USA., O'Connor DH; Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA., Sanders AD; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany., Korbel JO; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany., Ferguson B; Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA., Kubisch HM; Tulane National Primate Research Center, Covington, LA 70433, USA., Picker L; Oregon National Primate Research Center and Vaccine and Gene Therapy Institute, Oregon Health Sciences University, Beaverton, OR 97006, USA., Kalin NH; Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53719, USA., Rosene D; Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA., Levine J; Department of Neuroscience, University of Wisconsin, Madison, WI 53175, USA.; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA., Abbott DH; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.; Department of Obstetrics and Gynecology, Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA., Gray SB; The University of Texas MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, TX 78602, USA., Sanchez MM; Yerkes National Primate Research Center, Atlanta, GA 30329, USA.; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA., Kovacs-Balint ZA; Yerkes National Primate Research Center, Atlanta, GA 30329, USA., Kemnitz JW; Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.; Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA., Thomasy SM; Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.; Department of Ophthalmology and Vision Science, School of Medicine, University of California-Davis, Davis, CA 95817, USA., Roberts JA; California National Primate Research Center, Davis, CA 95616, USA., Kinnally EL; California National Primate Research Center, Davis, CA 95616, USA.; Department of Psychology, University of California, Davis, CA 95616, USA., Capitanio JP; California National Primate Research Center, Davis, CA 95616, USA.; Department of Psychology, University of California, Davis, CA 95616, USA., Skene JHP; Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA., Platt M; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA., Cole SA; Population Health Program, Texas Biomedical Research Institute and Southwest National Primate Research Center, San Antonio, TX 78227, USA., Green RE; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Ventura M; Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy., Wiseman RW; Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA., Paten B; Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA., Batzer MA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA., Rogers J; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. warrenwc@missouri.edu jr13@bcm.edu eee@gs.washington.edu., Eichler EE; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. warrenwc@missouri.edu jr13@bcm.edu eee@gs.washington.edu.; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Jazyk: angličtina
Zdroj: Science (New York, N.Y.) [Science] 2020 Dec 18; Vol. 370 (6523).
DOI: 10.1126/science.abc6617
Abstrakt: The rhesus macaque ( Macaca mulatta ) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.
(Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje