Nature 456, 239-244 (13 November 2008) | doi:10.1038/nature07410; Received 20 June 2008; Accepted 8 September 2008; Published online 15 October 2008

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Chris Bowler1,2, Andrew E. Allen1,3, Jonathan H. Badger3, Jane Grimwood4, Kamel Jabbari1, Alan Kuo5, Uma Maheswari1, Cindy Martens6, Florian Maumus1, Robert P. Otillar5, Edda Rayko1, Asaf Salamov5, Klaas Vandepoele6, Bank Beszteri7, Ansgar Gruber8, Marc Heijde1, Michael Katinka9, Thomas Mock10,32, Klaus Valentin7, Fréderic Verret11, John A. Berges12, Colin Brownlee11, Jean-Paul Cadoret13, Anthony Chiovitti14, Chang Jae Choi12, Sacha Coesel2,32, Alessandra De Martino1, J. Chris Detter5, Colleen Durkin10, Angela Falciatore2, Jérome Fournet15, Miyoshi Haruta16, Marie J. J. Huysman6,17, Bethany D. Jenkins18, Katerina Jiroutova19, Richard E. Jorgensen20, Yolaine Joubert15, Aaron Kaplan21, Nils Kröger22, Peter G. Kroth8, Julie La Roche23, Erica Lindquist5, Markus Lommer23, Véronique Martin–Jézéquel15, Pascal J. Lopez1, Susan Lucas5, Manuela Mangogna2, Karen McGinnis20, Linda K. Medlin7,11, Anton Montsant1,2, Marie-Pierre Oudot–Le Secq24, Carolyn Napoli20, Miroslav Obornik19, Micaela Schnitzler Parker10, Jean-Louis Petit9, Betina M. Porcel9, Nicole Poulsen25, Matthew Robison16, Leszek Rychlewski26, Tatiana A. Rynearson27, Jeremy Schmutz4, Harris Shapiro5, Magali Siaut2,32, Michele Stanley28, Michael R. Sussman16, Alison R. Taylor11,29, Assaf Vardi1,30, Peter von Dassow31, Wim Vyverman17, Anusuya Willis14, Lucjan S. Wyrwicz26, Daniel S. Rokhsar5, Jean Weissenbach9, E. Virginia Armbrust10, Beverley R. Green24, Yves Van de Peer6 & Igor V. Grigoriev5

  1. CNRS UMR8186, Department of Biology, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
  2. Stazione Zoologica 'Anton Dohrn', Villa Comunale, I-80121 Naples, Italy
  3. J. Craig Venter Institute, San Diego, California 92121, USA
  4. Joint Genome Institute-Stanford, Stanford Human Genome Center, 975 California Avenue, Palo Alto, California 94304, USA
  5. Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
  6. VIB Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
  7. Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
  8. Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany
  9. Genoscope, CEA-Institut de Génomique, UMR CNRS no. 8030, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
  10. School of Oceanography, University of Washington, Seattle, Washington 98195, USA
  11. Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
  12. Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, USA
  13. PBA, IFREMER, BP 21105, 44311 Nantes Cedex 03, France
  14. School of Botany, The University of Melbourne, Victoria 3010, Australia
  15. EA 2160, Laboratoire 'Mer, Molécule, Santé', Faculté des Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière, 44322, BP 92208, 44322 Nantes Cedex 3, France
  16. University of Wisconsin Biotechnology Center, 425 Henry Mall, Madison, Wisconsin 53706, USA
  17. Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000 Ghent, Belgium
  18. Department of Cell and Molecular Biology and Graduate School of Oceanography, University of Rhode Island, 316 Morrill Hall, 45 Lower College Road, Kingston, Rhode Island 02881, USA
  19. Biology Centre ASCR, Institute of Parasitology and University of South Bohemia, Faculty of Science, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
  20. Bio5 Institute and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85719, USA
  21. Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
  22. School of Chemistry and Biochemistry, School of Materials Science and Engineering, School of Biology, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, USA
  23. Leibniz-Institut für Meereswissenschaften, 24105 Kiel, Germany
  24. Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
  25. School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
  26. BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland
  27. Graduate School of Oceanography, University of Rhode Island, South Ferry Road, Narragansett, Rhode Island 02882-1197, USA
  28. Microbial & Molecular Biology, Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, UK
  29. Department of Biology and Marine Biology, The University of North Carolina Wilmington, 601 South College Road, Wilmington, North Carolina 28403, USA
  30. Environmental Biophysics and Molecular Ecology Group, Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, New Jersey 08901, USA
  31. CNRS UMR7144, Station Biologique de Roscoff, Place George Teissier BP74, 29682 Roscoff Cedex, France
  32. Present addresses: University of East Anglia, School of Environmental Sciences, Norwich NR4 7TJ, UK (T.M.); Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA (S.C.); CEA, DSV, IBEB, SBVME, UMR 6191 CNRS/CEA/Université Aix-Marseille, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, Cadarache, Saint-Paul-lez-Durance F-13108, France (M.S.).

Correspondence to: Chris Bowler1,2 Correspondence and requests for materials should be addressed to C.B. (Email: cbowler@biologie.ens.fr).

This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth1, 2. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology3, 4, 5. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (approx40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.


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