The amphioxus genome and the evolution of the chordate karyotype

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-Gutiérrez, Inna Dubchak, Jordi Garcia-Fernàndez, Jeremy J. Gibson-Brown, Igor V. Grigoriev, Amy C. Horton, Pieter J. de Jong, Jerzy Jurka, Vladimir V. Kapitonov, Yuji Kohara, Yoko Kuroki, Erika Lindquist, Susan Lucas, Kazutoyo Osoegawa, Len A. Pennacchio, Asaf A. Salamov, Yutaka Satou, Tatjana Sauka-Spengler, Jeremy Schmutz, Tadasu Shin-I, Atsushi Toyoda, Marianne Bronner-Fraser, Asao Fujiyama, Linda Z. Holland, Peter W. H. Holland, Nori Satoh () and Daniel S. Rokhsar ()
Additional contact information
Nicholas H. Putnam: Department of Energy Joint Genome Institute
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
Marc Robinson-Rechavi: University of Lausanne
Eiichi Shoguchi: Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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
Igor V. Grigoriev: Department of Energy Joint Genome Institute
Amy C. Horton: Washington University in St Louis, St Louis, Missouri 63130, USA
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
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
Daniel S. Rokhsar: Department of Energy Joint Genome Institute

Nature, 2008, vol. 453, issue 7198, 1064-1071

Abstract: 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.

Date: 2008
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DOI: 10.1038/nature06967

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