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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Author

Listed:
  • Tarjei S. Mikkelsen

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA)

  • Matthew J. Wakefield

    (The Walter & Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3050, Australia)

  • Bronwen Aken

    (The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Chris T. Amemiya

    (Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, Washington 98101, USA)

  • Jean L. Chang

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Shannon Duke

    (College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USA)

  • Manuel Garber

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Andrew J. Gentles

    (Stanford University School of Medicine, P060 Lucas Center, Stanford, California 94305, USA
    Genetic Information Research Institute, 1925 Landings Drive, Mountain View, California 94043, USA)

  • Leo Goodstadt

    (MRC Functional Genetics Unit, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK)

  • Andreas Heger

    (MRC Functional Genetics Unit, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK)

  • Jerzy Jurka

    (Genetic Information Research Institute, 1925 Landings Drive, Mountain View, California 94043, USA)

  • Michael Kamal

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Evan Mauceli

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Stephen M. J. Searle

    (The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Ted Sharpe

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Michelle L. Baker

    (Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA)

  • Mark A. Batzer

    (Biological Computation and Visualization Center, Center for Bio-Modular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA)

  • Panayiotis V. Benos

    (University of Pittsburgh, 3501 Fifth Avenue, Suite 3064, BST3, Pittsburgh, Pennsylvania 15260, USA)

  • Katherine Belov

    (Faculty of Veterinary Science, University of Sydney, New South Wales 2006, Australia)

  • Michele Clamp

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • April Cook

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • James Cuff

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Radhika Das

    (Duke University Medical Center, Box 3433, Durham, North Carolina 27710, USA)

  • Lance Davidow

    (Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA)

  • Janine E. Deakin

    (ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia)

  • Melissa J. Fazzari

    (Albert Einstein College of Medicine, Ullmann 911, 1300 Morris Park Avenue, Bronx, New York 10461, USA)

  • Jacob L. Glass

    (Albert Einstein College of Medicine, Ullmann 911, 1300 Morris Park Avenue, Bronx, New York 10461, USA)

  • Manfred Grabherr

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • John M. Greally

    (Albert Einstein College of Medicine, Ullmann 911, 1300 Morris Park Avenue, Bronx, New York 10461, USA)

  • Wanjun Gu

    (University of Colorado Health Sciences Center, MS 8101, 12801 17th Avenue, Aurora, Colorado 80045, USA)

  • Timothy A. Hore

    (ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia)

  • Gavin A. Huttley

    (John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia)

  • Michael Kleber

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Randy L. Jirtle

    (Duke University Medical Center, Box 3433, Durham, North Carolina 27710, USA)

  • Edda Koina

    (ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia)

  • Jeannie T. Lee

    (Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA)

  • Shaun Mahony

    (University of Pittsburgh, 3501 Fifth Avenue, Suite 3064, BST3, Pittsburgh, Pennsylvania 15260, USA)

  • Marco A. Marra

    (Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, British Columbia V5Z 4S6, Canada)

  • Robert D. Miller

    (Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA)

  • Robert D. Nicholls

    (Research Center Children’s Hospital of Pittsburgh, 3460 Fifth Avenue, Room 2109, Rangos, Pittsburgh, Pennsylvania 15213, USA)

  • Mayumi Oda

    (Albert Einstein College of Medicine, Ullmann 911, 1300 Morris Park Avenue, Bronx, New York 10461, USA)

  • Anthony T. Papenfuss

    (The Walter & Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3050, Australia)

  • Zuly E. Parra

    (Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA)

  • David D. Pollock

    (University of Colorado Health Sciences Center, MS 8101, 12801 17th Avenue, Aurora, Colorado 80045, USA)

  • David A. Ray

    (West Virginia University, Morgantown, West Virginia 26505, USA)

  • Jacqueline E. Schein

    (Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, British Columbia V5Z 4S6, Canada)

  • Terence P. Speed

    (The Walter & Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3050, Australia)

  • Katherine Thompson

    (ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia)

  • John L. VandeBerg

    (Southwest Foundation for Biomedical Research, San Antonio, Texas 78245, USA)

  • Claire M. Wade

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA)

  • Jerilyn A. Walker

    (Biological Computation and Visualization Center, Center for Bio-Modular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA)

  • Paul D. Waters

    (ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia)

  • Caleb Webber

    (MRC Functional Genetics Unit, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK)

  • Jennifer R. Weidman

    (Duke University Medical Center, Box 3433, Durham, North Carolina 27710, USA)

  • Xiaohui Xie

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Michael C. Zody

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Jennifer A. Marshall Graves

    (ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia)

  • Chris P. Ponting

    (MRC Functional Genetics Unit, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK)

  • Matthew Breen

    (College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USA
    Center for Comparative Medicine and Translational Research, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USA)

  • Paul B. Samollow

    (Texas A&M University, 4458 TAMU, College Station, Texas 77843, USA)

  • Eric S. Lander

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Kerstin Lindblad-Toh

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

Abstract

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian (‘marsupial’) species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

Suggested Citation

  • Tarjei S. Mikkelsen & Matthew J. Wakefield & Bronwen Aken & Chris T. Amemiya & Jean L. Chang & Shannon Duke & Manuel Garber & Andrew J. Gentles & Leo Goodstadt & Andreas Heger & Jerzy Jurka & Michael , 2007. "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences," Nature, Nature, vol. 447(7141), pages 167-177, May.
    • Handle: RePEc:nat:nature:v:447:y:2007:i:7141:d:10.1038_nature05805
    DOI: 10.1038/nature05805
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    Cited by:

    1. Donna M. Bond & Oscar Ortega-Recalde & Melanie K. Laird & Takashi Hayakawa & Kyle S. Richardson & Finlay.C. B. Reese & Bruce Kyle & Brooke E. McIsaac-Williams & Bruce C. Robertson & Yolanda Heezik & A, 2023. "The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Cassie L. Kemmler & Jana Smolikova & Hannah R. Moran & Brandon J. Mannion & Dunja Knapp & Fabian Lim & Anna Czarkwiani & Viviana Hermosilla Aguayo & Vincent Rapp & Olivia E. Fitch & Seraina Bötschi & , 2023. "Conserved enhancers control notochord expression of vertebrate Brachyury," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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