Title

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

Authors

Wesley C. Warren, 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.
R Alan Harris, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Marina Haukness, Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Ian T. Fiddes, Inscripta Inc., Boulder, CO 80301, USA.
Shwetha C. Murali, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Jason Fernandes, Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Philip C. Dishuck, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Jessica M. Storer, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Muthuswamy Raveendran, Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
LaDeana W. Hillier, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
David Porubsky, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Yafei Mao, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
David Gordon, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Mitchell R. Vollger, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Alexandra P. Lewis, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Katherine M. Munson, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Elizabeth DeVogelaere, Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Joel Armstrong, Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Mark Diekhans, Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Jerilyn A. Walker, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Chad Tomlinson, McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA.
Tina A. Graves-Lindsay, McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA.
Milinn Kremitzki, McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA.
Sofie R. Salama, Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Peter A. Audano, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Merly Escalona, Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Nicholas W. Maurer, Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.
Francesca Antonacci, Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Ludovica Mercuri, Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Flavia A. Maggiolini, Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Claudia Rita Catacchio, Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy.
Jason G. Underwood, Pacific Biosciences of California, Seattle, WA 94025, USA.
David H. O'Connor, Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA.

Document Type

Article

Publication Date

12-18-2020

Abstract

The rhesus macaque () 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.

Publication Source (Journal or Book title)

Science (New York, N.Y.)

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