The $Phaeodactylum$ genome reveals the evolutionary history of diatom genomes

Chris Bowler 1, * Andrew E. Allen 1, 2 Jonathan H. Badger 2 Jane Grimwood 3 Kamel Jabbari 1 Alan Kuo 4 Uma Maheswari 1 Cindy Martens 5 Florian Maumus 6 Robert P. Otillar Edda Rayko 1 Asaf Salamov 3 Klaas Vandepoele 7 Bank Beszteri 8 Ansgar Gruber Marc Heijde 9 Michael Katinka 10 Thomas Mock 11 Klaus Valentin 8 Fréderic Verret John A. Berges Colin Brownlee 12 Jean-Paul Cadoret 13 Anthony Chiovitti Chang Jae Choi Sacha Coesel 11, 14 Alessandra de Martino 15 J. Chris Detter Colleen Durkin Angela Falciatore 14, 16 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 17 Erica Lindquist Markus Lommer Véronique Martin-Jézéquel Pascal J. Lopez 1 Susan Lucas 3 Manuela Mangogna Karen Mcginnis Linda K. Medlin Anton Montsant Marie-Pierre Oudot-Le Secq Carolyn Napoli 18 Miroslav Obornik Micaela Schnitzler Parker 19 Jean-Louis Petit 10 Betina M. Porcel 10 Nicole Poulsen Matthew Robison Leszek Rychlewski Tatiana A. Rynearson Jeremy Schmutz 3, 20 Harris Shapiro 3 Magali Siaut 11 Michele Stanley Michael R. Sussman Alison R. Taylor Assaf Vardi 15 Peter von Dassow 21 Wim Vyverman Anusuya Willis Lucjan S. Wyrwicz Daniel S. Rokhsar Jean Weissenbach 10 E. Virginia Armbrust Beverley R. Green Yves van de Peer 5 Igor V. Grigoriev
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 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 (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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Chris Bowler, Andrew E. Allen, Jonathan H. Badger, Jane Grimwood, Kamel Jabbari, et al.. The $Phaeodactylum$ genome reveals the evolutionary history of diatom genomes. Nature, Nature Publishing Group, 2008, 456 (7410), pp.239-244. ⟨10.1038/nature07410⟩. ⟨cea-00910244⟩

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