The genome of the vervet ( Chlorocebus aethiops sabaeus )
| Autor: | Nicoletta Archidiacono, Jennifer F. Hughes, George M. Weinstock, Yoon Jung, Christopher A. Schmitt, Angela Noll, Nelson B. Freimer, Matthew J. Jorgensen, Jennifer J. Tuscher, Nam Tran, Jason M. Brenchley, David H. O’Connor, Matthew W. Hahn, Eugene Redmond, Alex Nisbett, Roland Zahn, Hannes Svardal, Gary P. Schroth, Raquel García-Pérez, Magnus Nordborg, Nikoleta Juretic, Michael J. Montague, Gregg W.C. Thomas, Michel M. Dione, Julie A. Karl, Anna J. Jasinska, Wesley C. Warren, Jay R. Kaplan, Richard K. Wilson, Patrick Minx, Bronwen Aken, Mariano Rocchi, Colby Chiang, Françoise Thibaud-Nissen, Jessica Wasserscheid, Vasily Ramensky, Oi Wa Choi, Gennady Churakov, Roscoe Stanyon, Yu S. Huang, David Webb, Brian J. Raney, Jörn E. Schmitz, Milinn Kremitzki, Beatrice Jacquelin, Michaela Müller-Trutwin, Juergen Schmitz, Rishi Nag, Tomas Marques-Bonet, LaDeana W. Hillier, Martin Antonio, Tina Graves, Trudy R. Turner, Kim Kyung, Ken Dewar, Chad Tomlinson, Roger W. Wiseman, Oronzo Capozzi |
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| Přispěvatelé: | The McDonnell Genome Institute (MGI), Washington University in Saint Louis (WUSTL), Semel Institute for Neuroscience and Human Behavior [Los Angeles, Ca], University of California [Los Angeles] (UCLA), University of California-University of California, Institute of Bioorganic Chemistry [Poznań], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institució Catalana de Recerca i Estudis Avançats (ICREA), Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Bari Aldo Moro (UNIBA), Whitehead Institute, Massachusetts Institute of Technology (MIT), McGill University = Université McGill [Montréal, Canada], University of Wisconsin - Milwaukee, University of the Free State [South Africa], University of Wisconsin-Madison, Beth Israel Deaconess Medical Center [Boston] (BIDMC), Harvard Medical School [Boston] (HMS), Crucell Holland B.V, St. Kitts Biomedical Research Foundation, Régulation des Infections Rétrovirales, Institut Pasteur [Paris], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Medical Research Council Unit The Gambia (MRC), Illumina Incorporated [San Diego, CA, USA], Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center, Indiana University [Bloomington], Indiana University System, University of California [Santa Cruz] (UCSC), University of California, European Molecular Biology Laboratory [Hinxton], Institute of Experimental Pathology (ZMBE), Westfälische Wilhelms-Universität Münster (WWU), Institute for Evolution and Biodiversity (IEB), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), National Center for Biotechnology Information (NCBI), The Jackson Laboratory [Bar Harbor] (JAX), Funding to R.K.W. was provided by NIH-NHGRI grant 5U54HG00307907. Support for the Vervet Research Colony was provided by NIH grant RR019963/OD010965 to J.R.K. Funding to N.B.F. was provided by NIH grants R01RR016300 and R01OD010980. The French National Agency for Research on AIDS and Viral Hepatitis (ANRS) provided funding to M.C.M.-T. Funding to M.R. and R.S. was provided by the Ministero della Universita’ e della Ricerca. Funding to K.D. was provided by Genome Canada and Genome Quebec. B.A. and R.N. acknowledge support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory., We thank the following organizations for providing sampling permits and permissions: Ethiopian Wildlife Conservation Authority, Zambia Wildlife Authority, Wildlife Division, Forestry Commission, Republic of Ghana, and Gambia Department of Parks and Wildlife Management. We thank Dr. James L. Blanchard and Dr. Ivona Pandrea for vervet samples used to characterize MHC. We thank Josh McMichael and Josh Peck for figure assistance. We thank Joanne Nelson and Barbara Gillam for data submission. We thank the members of the library production group led by Catrina Fronick and sequencing led by Matt Cordes. We also thank the Medical Research Council Unit (MRC), The Gambia for their assistance, as well as all the veterinarians who worked with us to safely obtain samples., National Institutes of Health (US), National Human Genome Research Institute (US), Agence Nationale de Recherches sur le SIDA et les Hépatites Virales (France), Agence Nationale de la Recherche (France), Ministero dell'Istruzione, dell'Università e della Ricerca, Genome Canada, EMBO, Wellcome Trust, University of California (UC)-University of California (UC), Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), University of the Free State [South Africa] (UFS), Institut Pasteur [Paris] (IP), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Università degli Studi di Firenze = University of Florence (UniFI) |
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
animal diseases
[SDV]Life Sciences [q-bio] Chlorocebus aethiops Cercopithecus aethiops Medical and Health Sciences Major Histocompatibility Complex MESH: Animals MESH: Genetic Variation MESH: Phylogeny Genetics (clinical) Phylogeny MESH: Evolution Molecular Gene Rearrangement education.field_of_study Cercopithecini Genome biology MESH: Genomics [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] MESH: Karyotype Genomics Biological Sciences 3. Good health Rhesus macaque Phylogeography MESH: Phylogeography [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology [SDE]Environmental Sciences Complete Genome assembly primates cercopithecini Infection Biotechnology MESH: Computational Biology Resource Evolution Bioinformatics MESH: Gene Rearrangement Population Karyotype Simis Old World monkey MESH: Molecular Sequence Annotation [SDV.BID]Life Sciences [q-bio]/Biodiversity Chromosome Painting Evolution Molecular MESH: Major Histocompatibility Complex [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] parasitic diseases Genetics Animals MESH: Genome [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology education [SDV.GEN]Life Sciences [q-bio]/Genetics Genètica animal MESH: Chromosome Painting Human Genome Molecular Computational Biology Genetic Variation Molecular Sequence Annotation Gene rearrangement biology.organism_classification MESH: Cercopithecus aethiops [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics Evolutionary biology African Green Monkey |
| Zdroj: | Genome Research Genome Research, Cold Spring Harbor Laboratory Press, 2015, 25 (12), pp.1921-1933. ⟨10.1101/gr.192922.115⟩ Digital.CSIC. Repositorio Institucional del CSIC instname Genome Research, 2015, 25 (12), pp.1921-1933. ⟨10.1101/gr.192922.115⟩ Recercat. Dipósit de la Recerca de Catalunya Genome research, vol 25, iss 12 |
| ISSN: | 1088-9051 1549-5469 |
| DOI: | 10.1101/gr.192922.115⟩ |
| Popis: | Warren, Wesley C. et al. We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations. Funding to R.K.W. was provided by NIH-NHGRI grant 5U54HG00307907. Support for the Vervet Research Colony was provided by NIH grant RR019963/OD010965 to J.R.K. Funding to N.B.F. was provided by NIH grants R01RR016300 and R01OD010980. The French National Agency for Research on AIDS and Viral Hepatitis (ANRS) provided funding to M.C.M.-T. Funding to M.R. and R.S. was provided by the Ministero della Universita’ e della Ricerca. Funding to K.D. was provided by Genome Canada and Genome Quebec. B.A. and R.N. acknowledge support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory. |
| Databáze: | OpenAIRE |
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