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The amphioxus genome and the evolution of the chordate karyotype

Author

Listed:
  • Nicholas H. Putnam

    (Department of Energy Joint Genome Institute
    Center for Integrative Genomics, University of California, Berkeley, California 94720, USA)

  • Thomas Butts

    (University of Oxford, South Parks Road, Oxford OX1 3PS, UK)

  • David E. K. Ferrier

    (The Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife KY16 8LB, UK)

  • Rebecca F. Furlong

    (University of Oxford, South Parks Road, Oxford OX1 3PS, UK)

  • Uffe Hellsten

    (Department of Energy Joint Genome Institute)

  • Takeshi Kawashima

    (Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
    Present addresses: Okinawa Institute of Science and Technology (OIST), Uruma, Okinawa 904-2234, Japan (T.K., E.S. and N.S.); Genome Sequencing Center, Department of Genetics, Washington University in St Louis School of Medicine, St Louis, Missouri 63108, USA (A.C.H.); Institute for Evolutionary Discovery, 909 Hiawatha Drive, Mount Pleasant, Michigan 48858, USA (J.J.G-B.).)

  • Marc Robinson-Rechavi

    (University of Lausanne
    Swiss Institute of Bioinformatics)

  • Eiichi Shoguchi

    (Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
    Present addresses: Okinawa Institute of Science and Technology (OIST), Uruma, Okinawa 904-2234, Japan (T.K., E.S. and N.S.); Genome Sequencing Center, Department of Genetics, Washington University in St Louis School of Medicine, St Louis, Missouri 63108, USA (A.C.H.); Institute for Evolutionary Discovery, 909 Hiawatha Drive, Mount Pleasant, Michigan 48858, USA (J.J.G-B.).)

  • Astrid Terry

    (Department of Energy Joint Genome Institute)

  • Jr-Kai Yu

    (California Institute of Technology, Pasadena, California 91125, USA)

  • E`lia Benito-Gutiérrez

    (National Institute for Medical Research, Mill Hill, London NW7 1AA, UK)

  • Inna Dubchak

    (Department of Energy Joint Genome Institute)

  • Jordi Garcia-Fernàndez

    (Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 645, Barcelona 08028, Spain)

  • Jeremy J. Gibson-Brown

    (Washington University in St Louis, St Louis, Missouri 63130, USA
    Present addresses: Okinawa Institute of Science and Technology (OIST), Uruma, Okinawa 904-2234, Japan (T.K., E.S. and N.S.); Genome Sequencing Center, Department of Genetics, Washington University in St Louis School of Medicine, St Louis, Missouri 63108, USA (A.C.H.); Institute for Evolutionary Discovery, 909 Hiawatha Drive, Mount Pleasant, Michigan 48858, USA (J.J.G-B.).)

  • Igor V. Grigoriev

    (Department of Energy Joint Genome Institute)

  • Amy C. Horton

    (Washington University in St Louis, St Louis, Missouri 63130, USA
    Present addresses: Okinawa Institute of Science and Technology (OIST), Uruma, Okinawa 904-2234, Japan (T.K., E.S. and N.S.); Genome Sequencing Center, Department of Genetics, Washington University in St Louis School of Medicine, St Louis, Missouri 63108, USA (A.C.H.); Institute for Evolutionary Discovery, 909 Hiawatha Drive, Mount Pleasant, Michigan 48858, USA (J.J.G-B.).)

  • Pieter J. de Jong

    (Children’s Hospital of Oakland Research Institute, Oakland, California 94609, USA)

  • Jerzy Jurka

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

  • Vladimir V. Kapitonov

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

  • Yuji Kohara

    (National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan)

  • Yoko Kuroki

    (RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Erika Lindquist

    (Department of Energy Joint Genome Institute)

  • Susan Lucas

    (Department of Energy Joint Genome Institute)

  • Kazutoyo Osoegawa

    (Children’s Hospital of Oakland Research Institute, Oakland, California 94609, USA)

  • Len A. Pennacchio

    (Department of Energy Joint Genome Institute)

  • Asaf A. Salamov

    (Department of Energy Joint Genome Institute)

  • Yutaka Satou

    (Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan)

  • Tatjana Sauka-Spengler

    (California Institute of Technology, Pasadena, California 91125, USA)

  • Jeremy Schmutz

    (JGI Stanford Human Genome Center, 975 California Avenue, Palo Alto, California 94304, USA)

  • Tadasu Shin-I

    (National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan)

  • Atsushi Toyoda

    (RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Marianne Bronner-Fraser

    (California Institute of Technology, Pasadena, California 91125, USA)

  • Asao Fujiyama

    (RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
    National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan)

  • Linda Z. Holland

    (Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093-0202, USA)

  • Peter W. H. Holland

    (University of Oxford, South Parks Road, Oxford OX1 3PS, UK)

  • Nori Satoh

    (Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
    Present addresses: Okinawa Institute of Science and Technology (OIST), Uruma, Okinawa 904-2234, Japan (T.K., E.S. and N.S.); Genome Sequencing Center, Department of Genetics, Washington University in St Louis School of Medicine, St Louis, Missouri 63108, USA (A.C.H.); Institute for Evolutionary Discovery, 909 Hiawatha Drive, Mount Pleasant, Michigan 48858, USA (J.J.G-B.).)

  • Daniel S. Rokhsar

    (Department of Energy Joint Genome Institute
    Center for Integrative Genomics, University of California, Berkeley, California 94720, USA)

Abstract

Lancelets (‘amphioxus’) are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic ∼520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

Suggested Citation

  • Nicholas H. Putnam & Thomas Butts & David E. K. Ferrier & Rebecca F. Furlong & Uffe Hellsten & Takeshi Kawashima & Marc Robinson-Rechavi & Eiichi Shoguchi & Astrid Terry & Jr-Kai Yu & E`lia Benito-Gut, 2008. "The amphioxus genome and the evolution of the chordate karyotype," Nature, Nature, vol. 453(7198), pages 1064-1071, June.
    • Handle: RePEc:nat:nature:v:453:y:2008:i:7198:d:10.1038_nature06967
    DOI: 10.1038/nature06967
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    Cited by:

    1. Konstantin Gorbunov & Vassily Lyubetsky, 2020. "Linear Time Additively Exact Algorithm for Transformation of Chain-Cycle Graphs for Arbitrary Costs of Deletions and Insertions," Mathematics, MDPI, vol. 8(11), pages 1-30, November.
    2. Woranop Sukparangsi & Elena Morganti & Molly Lowndes & Hélène Mayeur & Melanie Weisser & Fella Hammachi & Hanna Peradziryi & Fabian Roske & Jurriaan Hölzenspies & Alessandra Livigni & Benoit Gilbert G, 2022. "Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    3. Caroline B. Albertin & Sofia Medina-Ruiz & Therese Mitros & Hannah Schmidbaur & Gustavo Sanchez & Z. Yan Wang & Jane Grimwood & Joshua J. C. Rosenthal & Clifton W. Ragsdale & Oleg Simakov & Daniel S. , 2022. "Genome and transcriptome mechanisms driving cephalopod evolution," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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