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

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 Kamal, Evan Mauceli, Stephen M. J. Searle, Ted Sharpe, Michelle L. Baker, Mark A. Batzer, Panayiotis V. Benos, Katherine Belov, Michele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E. Deakin, Melissa J. Fazzari, Jacob L. Glass, Manfred Grabherr, John M. Greally, Wanjun Gu, Timothy A. Hore, Gavin A. Huttley, Michael Kleber, Randy L. Jirtle, Edda Koina, Jeannie T. Lee, Shaun Mahony, Marco A. Marra, Robert D. Miller, Robert D. Nicholls, Mayumi Oda, Anthony T. Papenfuss, Zuly E. Parra, David D. Pollock, David A. Ray, Jacqueline E. Schein, Terence P. Speed, Katherine Thompson, John L. VandeBerg, Claire M. Wade, Jerilyn A. Walker, Paul D. Waters, Caleb Webber, Jennifer R. Weidman, Xiaohui Xie, Michael C. Zody, Jennifer A. Marshall Graves, Chris P. Ponting, Matthew Breen, Paul B. Samollow, Eric S. Lander () and Kerstin Lindblad-Toh ()
Additional contact information
Tarjei S. Mikkelsen: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, 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
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
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
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
Kerstin Lindblad-Toh: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

Nature, 2007, vol. 447, issue 7141, 167-177

Abstract: 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.

Date: 2007
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DOI: 10.1038/nature05805

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