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Escalona M, VanCampen J, Maurer NW, Haukness M, Okhovat M, Harris RS, Watwood A, Hartley GA, O’Neill RJ, Medvedev P, Makova KD, Vollmers C, Carbone L, Green RE. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J Hered 2023; 114:35-43. [PMID: 36146896 PMCID: PMC10019027 DOI: 10.1093/jhered/esac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/08/2022] [Indexed: 02/04/2023] Open
Abstract
The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.
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Affiliation(s)
- Merly Escalona
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jake VanCampen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - Marina Haukness
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Allison Watwood
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06296, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06296, USA
| | - Rachel J O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06296, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06296, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA
- Department of Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
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Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science 2021; 370:370/6523/eabc6617. [PMID: 33335035 DOI: 10.1126/science.abc6617] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022]
Abstract
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.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. .,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
| | - 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
| | | | - Shwetha C Murali
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, 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.,Institue for Systems Biology, Seattle, WA 98109, 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.,Howard Hughes Medical Institute, 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
| | | | - 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
| | | | - Ludovica Mercuri
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | | | | | | | - David H O'Connor
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | | | - Louis Picker
- Oregon National Primate Research Center and Vaccine and Gene Therapy Institute, Oregon Health Sciences University, Beaverton, OR 97006, USA
| | - Ned H Kalin
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53719, USA
| | - Douglas Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jon Levine
- Department of Neuroscience, University of Wisconsin, Madison, WI 53175, USA.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA
| | - David H Abbott
- 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
| | - Stanton B Gray
- The University of Texas MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, TX 78602, USA
| | - Mar M Sanchez
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
| | | | - Joseph W Kemnitz
- 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
| | - Sara M Thomasy
- 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
| | | | - Erin L Kinnally
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - John P Capitanio
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - J H Pate Skene
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute and Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mario Ventura
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Benedict Paten
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience 2020; 9:giaa029. [PMID: 32242610 PMCID: PMC7118895 DOI: 10.1093/gigascience/giaa029] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/08/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The development of trio binning as an approach for assembling diploid genomes has enabled the creation of fully haplotype-resolved reference genomes. Unlike other methods of assembly for diploid genomes, this approach is enhanced, rather than hindered, by the heterozygosity of the individual sequenced. To maximize heterozygosity and simultaneously assemble reference genomes for 2 species, we applied trio binning to an interspecies F1 hybrid of yak (Bos grunniens) and cattle (Bos taurus), 2 species that diverged nearly 5 million years ago. The genomes of both of these species are composed of acrocentric autosomes. RESULTS We produced the most continuous haplotype-resolved assemblies for a diploid animal yet reported. Both the maternal (yak) and paternal (cattle) assemblies have the largest 2 chromosomes in single haplotigs, and more than one-third of the autosomes similarly lack gaps. The maximum length haplotig produced was 153 Mb without any scaffolding or gap-filling steps and represents the longest haplotig reported for any species. The assemblies are also more complete and accurate than those reported for most other vertebrates, with 97% of mammalian universal single-copy orthologs present. CONCLUSIONS The high heterozygosity inherent to interspecies crosses maximizes the effectiveness of the trio binning method. The interspecies trio binning approach we describe is likely to provide the highest-quality assemblies for any pair of species that can interbreed to produce hybrid offspring that develop to sufficient cell numbers for DNA extraction.
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Affiliation(s)
- Edward S Rice
- Department of Animal Science, University of Nebraska–Lincoln, C203 ANSC, Lincoln, NE 68583, USA
- Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Michael P Heaton
- US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA
| | - Theodore S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA
| | | | | | - Derek M Bickhart
- Dairy Forage Research Center, 1925 Linden Drive, ARS USDA, Madison, WI 53706, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave., ARS USDA, Beltsville, MD 20705, USA
| | - Brian Vander Ley
- Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, 820 Road 313, Clay Center, NE 68933, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska–Lincoln, C203 ANSC, Lincoln, NE 68583, USA
| | - Timothy P L Smith
- US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA
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