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The African coelacanth genome provides insights into tetrapod evolution

Author

Listed:
  • Chris T. Amemiya

    (Molecular Genetics Program, Benaroya Research Institute
    University of Washington)

  • Jessica Alföldi

    (Broad Institute of MIT and Harvard)

  • Alison P. Lee

    (Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore)

  • Shaohua Fan

    (University of Konstanz)

  • Hervé Philippe

    (Université de Montréal, Centre Robert Cedergren, Montréal H3T 1J4, Canada)

  • Iain MacCallum

    (Broad Institute of MIT and Harvard)

  • Ingo Braasch

    (Institute of Neuroscience, University of Oregon)

  • Tereza Manousaki

    (University of Konstanz
    Konstanz Research School of Chemical Biology, University of Konstanz)

  • Igor Schneider

    (Instituto de Ciencias Biologicas, Universidade Federal do Para)

  • Nicolas Rohner

    (Harvard Medical School)

  • Chris Organ

    (University of Utah)

  • Domitille Chalopin

    (Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Superieure de Lyon, Lyon 69007, France)

  • Jeramiah J. Smith

    (University of Kentucky)

  • Mark Robinson

    (Molecular Genetics Program, Benaroya Research Institute)

  • Rosemary A. Dorrington

    (Biomedical Biotechnology Research Unit (BioBRU), Microbiology & Biotechnology, Rhodes University)

  • Marco Gerdol

    (University of Trieste)

  • Bronwen Aken

    (Wellcome Trust Sanger Institute)

  • Maria Assunta Biscotti

    (Polytechnic University of Marche)

  • Marco Barucca

    (Polytechnic University of Marche)

  • Denis Baurain

    (University of Liege)

  • Aaron M. Berlin

    (Broad Institute of MIT and Harvard)

  • Gregory L. Blatch

    (Biomedical Biotechnology Research Unit (BioBRU), Microbiology & Biotechnology, Rhodes University
    College of Health and Biomedicine, Victoria University)

  • Francesco Buonocore

    (Agro-food and Forest Systems, University of Tuscia)

  • Thorsten Burmester

    (University of Hamburg)

  • Michael S. Campbell

    (Eccles Institute of Human Genetics, University of Utah)

  • Adriana Canapa

    (Polytechnic University of Marche)

  • John P. Cannon

    (University of South Florida Morsani College of Medicine, Children’s Research Institute)

  • Alan Christoffels

    (South African National Bioinformatics Institute, University of the Western Cape)

  • Gianluca De Moro

    (University of Trieste)

  • Adrienne L. Edkins

    (Biomedical Biotechnology Research Unit (BioBRU), Microbiology & Biotechnology, Rhodes University)

  • Lin Fan

    (Broad Institute of MIT and Harvard)

  • Anna Maria Fausto

    (Agro-food and Forest Systems, University of Tuscia)

  • Nathalie Feiner

    (University of Konstanz
    International Max-Planck Research School for Organismal Biology, University of Konstanz)

  • Mariko Forconi

    (Polytechnic University of Marche)

  • Junaid Gamieldien

    (South African National Bioinformatics Institute, University of the Western Cape)

  • Sante Gnerre

    (Broad Institute of MIT and Harvard)

  • Andreas Gnirke

    (Broad Institute of MIT and Harvard)

  • Jared V. Goldstone

    (Woods Hole Oceanographic Institution)

  • Wilfried Haerty

    (MRC Functional Genomics Unit, Oxford University)

  • Mark E. Hahn

    (Woods Hole Oceanographic Institution)

  • Uljana Hesse

    (South African National Bioinformatics Institute, University of the Western Cape)

  • Steve Hoffmann

    (Transcriptome Bioinformatics Group, LIFE Research Center for Civilization Diseases, Universität Leipzig)

  • Jeremy Johnson

    (Broad Institute of MIT and Harvard)

  • Sibel I. Karchner

    (Woods Hole Oceanographic Institution)

  • Shigehiro Kuraku

    (University of Konstanz
    Present addresses: Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Kobe, Japan (S.K.); Boston Children’s Hospital, Boston, Massachusetts, USA (E.M.); Computational Biology Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Campus, Anzio Road, Observatory 7925, South Africa (S.P.); New York Genome Center, New York, New York, USA (F.J.R.).)

  • Marcia Lara

    (Broad Institute of MIT and Harvard)

  • Joshua Z. Levin

    (Broad Institute of MIT and Harvard)

  • Gary W. Litman

    (University of South Florida Morsani College of Medicine, Children’s Research Institute)

  • Evan Mauceli

    (Broad Institute of MIT and Harvard
    Present addresses: Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Kobe, Japan (S.K.); Boston Children’s Hospital, Boston, Massachusetts, USA (E.M.); Computational Biology Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Campus, Anzio Road, Observatory 7925, South Africa (S.P.); New York Genome Center, New York, New York, USA (F.J.R.).)

  • Tsutomu Miyake

    (Graduate School of Science and Technology, Keio University)

  • M. Gail Mueller

    (All Children’s Hospital)

  • David R. Nelson

    (Immunology and Biochemistry, University of Tennessee Health Science Center)

  • Anne Nitsche

    (Bioinformatics Group, Universität Leipzig)

  • Ettore Olmo

    (Polytechnic University of Marche)

  • Tatsuya Ota

    (The Graduate University for Advanced Studies)

  • Alberto Pallavicini

    (University of Trieste)

  • Sumir Panji

    (South African National Bioinformatics Institute, University of the Western Cape
    Present addresses: Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Kobe, Japan (S.K.); Boston Children’s Hospital, Boston, Massachusetts, USA (E.M.); Computational Biology Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Campus, Anzio Road, Observatory 7925, South Africa (S.P.); New York Genome Center, New York, New York, USA (F.J.R.).)

  • Barbara Picone

    (South African National Bioinformatics Institute, University of the Western Cape)

  • Chris P. Ponting

    (MRC Functional Genomics Unit, Oxford University)

  • Sonja J. Prohaska

    (Computational EvoDevo Group, Universität Leipzig)

  • Dariusz Przybylski

    (Broad Institute of MIT and Harvard)

  • Nil Ratan Saha

    (Molecular Genetics Program, Benaroya Research Institute)

  • Vydianathan Ravi

    (Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore)

  • Filipe J. Ribeiro

    (Broad Institute of MIT and Harvard
    Present addresses: Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Kobe, Japan (S.K.); Boston Children’s Hospital, Boston, Massachusetts, USA (E.M.); Computational Biology Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Campus, Anzio Road, Observatory 7925, South Africa (S.P.); New York Genome Center, New York, New York, USA (F.J.R.).)

  • Tatjana Sauka-Spengler

    (Weatherall Institute of Molecular Medicine, University of Oxford)

  • Giuseppe Scapigliati

    (Agro-food and Forest Systems, University of Tuscia)

  • Stephen M. J. Searle

    (Wellcome Trust Sanger Institute)

  • Ted Sharpe

    (Broad Institute of MIT and Harvard)

  • Oleg Simakov

    (University of Konstanz
    European Molecular Biology Laboratory)

  • Peter F. Stadler

    (Bioinformatics Group, Universität Leipzig)

  • John J. Stegeman

    (Woods Hole Oceanographic Institution)

  • Kenta Sumiyama

    (National Institute of Genetics)

  • Diana Tabbaa

    (Broad Institute of MIT and Harvard)

  • Hakim Tafer

    (Bioinformatics Group, Universität Leipzig)

  • Jason Turner-Maier

    (Broad Institute of MIT and Harvard)

  • Peter van Heusden

    (South African National Bioinformatics Institute, University of the Western Cape)

  • Simon White

    (Wellcome Trust Sanger Institute)

  • Louise Williams

    (Broad Institute of MIT and Harvard)

  • Mark Yandell

    (Eccles Institute of Human Genetics, University of Utah)

  • Henner Brinkmann

    (Université de Montréal, Centre Robert Cedergren, Montréal H3T 1J4, Canada)

  • Jean-Nicolas Volff

    (Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Superieure de Lyon, Lyon 69007, France)

  • Clifford J. Tabin

    (Harvard Medical School)

  • Neil Shubin

    (University of Chicago)

  • Manfred Schartl

    (Biocenter, University of Wuerzburg)

  • David B. Jaffe

    (Broad Institute of MIT and Harvard)

  • John H. Postlethwait

    (Institute of Neuroscience, University of Oregon)

  • Byrappa Venkatesh

    (Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore)

  • Federica Di Palma

    (Broad Institute of MIT and Harvard)

  • Eric S. Lander

    (Broad Institute of MIT and Harvard)

  • Axel Meyer

    (University of Konstanz
    Konstanz Research School of Chemical Biology, University of Konstanz
    International Max-Planck Research School for Organismal Biology, University of Konstanz)

  • Kerstin Lindblad-Toh

    (Broad Institute of MIT and Harvard
    Science for Life Laboratory, Uppsala University)

Abstract

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

Suggested Citation

  • Chris T. Amemiya & Jessica Alföldi & Alison P. Lee & Shaohua Fan & Hervé Philippe & Iain MacCallum & Ingo Braasch & Tereza Manousaki & Igor Schneider & Nicolas Rohner & Chris Organ & Domitille Chalopi, 2013. "The African coelacanth genome provides insights into tetrapod evolution," Nature, Nature, vol. 496(7445), pages 311-316, April.
    • Handle: RePEc:nat:nature:v:496:y:2013:i:7445:d:10.1038_nature12027
    DOI: 10.1038/nature12027
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    Cited by:

    1. Felipe O. Cerezer & Cristian S. Dambros & Marco T. P. Coelho & Fernanda A. S. Cassemiro & Elisa Barreto & James S. Albert & Rafael O. Wüest & Catherine H. Graham, 2023. "Accelerated body size evolution in upland environments is correlated with recent speciation in South American freshwater fishes," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Mengfan Lyu & Andrey G. Malyutin & Beth M. Stadtmueller, 2023. "The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. 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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