The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Chris Bowler; Andrew E. Allen; Jonathan H. Badger; Jane Grimwood; Kamel Jabbari; Alan Kuo; Uma Maheswari; Cindy Martens; Florian Maumus; Robert P. Otillar; Edda Rayko; Asaf Salamov; Klaas Vandepoele; Bank Beszteri; Ansgar Gruber; Marc Heijde; Michael Katinka; Thomas Mock; Klaus Valentin; Frederic Verret; John A. Berges; Colin Brownlee; Jean-Paul Cadoret; Anthony Chiovitti; Chang Jae Choi; Sacha Coesel; Alessandra De Martino; J. Chris Detter; Colleen Durkin; Angela Falciatore; Jerome Fournet; Miyoshi Haruta; Marie J. J. Huysman; Bethany D. Jenkins; Katerina Jiroutova; Richard E. Jorgensen; Yolaine Joubert; Aaron Kaplan; Nils Kroger; Peter G. Kroth; Julie La Roche; Erica Lindquist; Markus Lommer; Veronique Martin-Jezequel; Pascal J. Lopez; Susan Lucas; Manuela Mangogna; Karen McGinnis; Linda K. Medlin; Anton Montsant; Marie-Pierre Oudot-Le Secq; Carolyn Napoli; Miroslav Obornik; Micaela Schnitzler Parker; Jean-Louis Petit; Betina M. Porcel; Nicole Poulsen; Matthew Robison; Leszek Rychlewski; Tatiana A. Rynearson; Jeremy Schmutz; Harris Shapiro; Magali Siaut; Michele Stanley; Michael R. Sussman; Alison R. Taylor; Assaf Vardi; Peter von Dassow; Wim Vyverman; Anusuya Willis; Lucjan S. Wyrwicz; Daniel S. Rokhsar; Jean Weissenbach; E. Virginia Armbrust; Beverley R. Green; Yves Van de Peer; Igor V. Grigoriev; Joint Genome Institute (JGI)

doi:10.1038/nature07410

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The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Journal article

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Peer reviewed

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Chris Bowler, Andrew E. Allen, Jonathan H. Badger, Jane Grimwood, Kamel Jabbari, Alan Kuo, Uma Maheswari, Cindy Martens, Florian Maumus, Robert P. Otillar, …

Nature (London), Vol.456(7219), pp.239-244

13/11/2008

DOI: https://doi.org/10.1038/nature07410

PMID: 18923393

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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 Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). 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 (similar to 40%) 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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Title: The Phaeodactylum genome reveals the evolutionary history of diatom genomes
Creators - without role: Chris Bowler - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Andrew E. Allen - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Jonathan H. Badger - J. Craig Venter Institute
Jane Grimwood - Joint Genome Institute
Kamel Jabbari - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Alan Kuo - Joint Genome Institute
Uma Maheswari - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Cindy Martens - Plant
Florian Maumus - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Robert P. Otillar - Joint Genome Institute
Edda Rayko - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Asaf Salamov - Joint Genome Institute
Klaas Vandepoele - Plant
Bank Beszteri - Polar
Ansgar Gruber - University of Konstanz
Marc Heijde - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Michael Katinka - Evry
Thomas Mock - University of Washington
Klaus Valentin - Polar
Frederic Verret - Marine Biol Assoc United Kingdom Lab, Plymouth PL1 2PB, Devon, England
John A. Berges - Univ Wisconsin, Dept Biol Sci, Milwaukee, WI 53201 USA
Colin Brownlee - Marine Biol Assoc United Kingdom Lab, Plymouth PL1 2PB, Devon, England
Jean-Paul Cadoret - Ifremer
Anthony Chiovitti - University of Melbourne
Chang Jae Choi - Univ Wisconsin, Dept Biol Sci, Milwaukee, WI 53201 USA
Sacha Coesel - Stn Zool A Dohrn, I-80121 Naples, Italy
Alessandra De Martino - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
J. Chris Detter - Joint Genome Institute
Colleen Durkin - University of Washington
Angela Falciatore - Stn Zool A Dohrn, I-80121 Naples, Italy
Jerome Fournet - Nantes Université
Miyoshi Haruta - Univ Wisconsin, Ctr Biotechnol, Madison, WI 53706 USA
Marie J. J. Huysman - Plant
Bethany D. Jenkins - Univ Rhode Isl, Dept Cell & Mol Biol, Kingston, RI 02881 USA
Katerina Jiroutova - Acad Sci Czech Republic, Inst Parasitol, Ctr Biol, CR-37005 Ceske Budejovice, Czech Republic
Richard E. Jorgensen - University of Arizona
Yolaine Joubert - Nantes Université
Aaron Kaplan - Hebrew University of Jerusalem
Nils Kroger - Georgia Institute of Technology
Peter G. Kroth - University of Konstanz
Julie La Roche - Leibniz Inst Marine Sci, D-24105 Kiel, Germany
Erica Lindquist - Joint Genome Institute
Markus Lommer - Leibniz Inst Marine Sci, D-24105 Kiel, Germany
Veronique Martin-Jezequel - Nantes Université
Pascal J. Lopez - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Susan Lucas - Joint Genome Institute
Manuela Mangogna - Stn Zool A Dohrn, I-80121 Naples, Italy
Karen McGinnis - University of Arizona
Linda K. Medlin - Polar
Anton Montsant - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Marie-Pierre Oudot-Le Secq - University of British Columbia
Carolyn Napoli - University of Arizona
Miroslav Obornik - Acad Sci Czech Republic, Inst Parasitol, Ctr Biol, CR-37005 Ceske Budejovice, Czech Republic
Micaela Schnitzler Parker - University of Washington
Jean-Louis Petit - Evry
Betina M. Porcel - Evry
Nicole Poulsen - Georgia Institute of Technology
Matthew Robison - Univ Wisconsin, Ctr Biotechnol, Madison, WI 53706 USA
Leszek Rychlewski - BioInfoBank Institute
Tatiana A. Rynearson - Supreme Council Of Health
Jeremy Schmutz - Joint Genome Institute
Harris Shapiro - Joint Genome Institute
Magali Siaut - Stn Zool A Dohrn, I-80121 Naples, Italy
Michele Stanley - Dunstaffnage Marine Res Lab, Scottish Assoc Marine Sci, Oban PA37 1QA, Argyll, Scotland
Michael R. Sussman - Univ Wisconsin, Ctr Biotechnol, Madison, WI 53706 USA
Alison R. Taylor - Marine Biol Assoc United Kingdom Lab, Plymouth PL1 2PB, Devon, England
Assaf Vardi - Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France
Peter von Dassow - CNRS, Biol Stn, UMR7144, F-29682 Roscoff, France
Wim Vyverman - Univ Ghent, Lab Protistol & Aquat Ecol, B-9000 Ghent, Belgium
Anusuya Willis - University of Melbourne
Lucjan S. Wyrwicz - BioInfoBank Institute
Daniel S. Rokhsar - Joint Genome Institute
Jean Weissenbach - Evry
E. Virginia Armbrust - University of Washington
Beverley R. Green - University of British Columbia
Yves Van de Peer - Plant
Igor V. Grigoriev - Joint Genome Institute
Joint Genome Institute (JGI)
Publication Details: Nature (London), Vol.456(7219), pp.239-244
Publisher: Springer Nature
Number of pages: 6
Grant note: ATIP 'Blanche' mba010002; dml010007 / NERC; UK Research & Innovation (UKRI); Natural Environment Research Council (NERC) mba010002; dml010007 / Natural Environment Research Council; UK Research & Innovation (UKRI); Natural Environment Research Council (NERC) LSHG-CT-2004-512035 / EU-funded FP6 Diatomics; European Union (EU) GOCE-CT-2004-505403 / EU-FP6 Marine Genomics Network of Excellence; European Union (EU) CNRS (France); Centre National de la Recherche Scientifique (CNRS) Agence Nationale de la Recherche (France); Agence Nationale de la Recherche (ANR)
Identifiers: 9943992008331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article