JOURNAL ARTICLE

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, Fréderic 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, Jérome Fournet, Miyoshi Haruta, Marie J J Huysman, Bethany D Jenkins, Katerina Jiroutova, Richard E Jorgensen, Yolaine Joubert, Aaron Kaplan, Nils Kröger, Peter G Kroth, Julie La Roche, Erica Lindquist, Markus Lommer, Véronique Martin-Jézéquel, 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
Nature 2008 November 13, 456 (7219): 239-44
18923393
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. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. 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 ( approximately 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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