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The Phaeodactylum genome reveals the evolutionary history of diatom genomes

The Phaeodactylum genome reveals the evolutionary history of diatom genomes
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
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 (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.

0028-0836
239-244
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Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, De Martino, Alessandra, Detter, J. Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, Huysman, Marie J. J., Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, Kroth, Peter G., La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin–Jézéquel, Véronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Secq, Marie-Pierre Oudot–Le, Napoli, Carolyn, Obornik, Miroslav, Parker, Micaela Schnitzler, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele, Sussman, Michael R., Taylor, Alison R., Vardi, Assaf, von Dassow, Peter, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Van de Peer, Yves and Grigoriev, Igor V. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature, 456 (7219), 239-244. (doi:10.1038/nature07410).

Record type: Article

Abstract

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 (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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Published date: 13 November 2008
Organisations: Ocean and Earth Science

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Local EPrints ID: 340282
URI: https://eprints.soton.ac.uk/id/eprint/340282
ISSN: 0028-0836
PURE UUID: 650cead2-069f-4508-9de4-4e0cfe81c6a3

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Date deposited: 18 Jun 2012 14:21
Last modified: 18 Jul 2017 05:45

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Contributors

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

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