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The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) NATURE. 456(7219). p.239-244
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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(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.
Keywords
THALASSIOSIRA-PSEUDONANA, RECIPROCAL GENE LOSS, BACILLARIOPHYCEAE, METABOLISM, MECHANISMS, COMPONENTS, BACTERIA, YEASTS

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MLA
Bowler, Chris, Andrew E Allen, Jonathan H Badger, et al. “The Phaeodactylum Genome Reveals the Evolutionary History of Diatom Genomes.” NATURE 456.7219 (2008): 239–244. Print.
APA
Bowler, Chris, Allen, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheswari, U., et al. (2008). The Phaeodactylum genome reveals the evolutionary history of diatom genomes. NATURE, 456(7219), 239–244.
Chicago author-date
Bowler, Chris, Andrew E Allen, Jonathan H Badger, Jane Grimwood, Kamel Jabbari, Alan Kuo, Uma Maheswari, et al. 2008. “The Phaeodactylum Genome Reveals the Evolutionary History of Diatom Genomes.” Nature 456 (7219): 239–244.
Chicago author-date (all authors)
Bowler, Chris, 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 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, and Igor V Grigoriev. 2008. “The Phaeodactylum Genome Reveals the Evolutionary History of Diatom Genomes.” Nature 456 (7219): 239–244.
Vancouver
1.
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. NATURE. 2008;456(7219):239–44.
IEEE
[1]
C. Bowler et al., “The Phaeodactylum genome reveals the evolutionary history of diatom genomes,” NATURE, vol. 456, no. 7219, pp. 239–244, 2008.
@article{445404,
  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(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.},
  author       = {Bowler, Chris and Allen, Andrew E and Badger, Jonathan H and Grimwood, Jane and Jabbari, Kamel and Kuo, Alan and Maheswari, Uma and Martens, Cindy and Maumus, Florian and Otillar, Robert P and Rayko, Edda and Salamov, Asaf and Vandepoele, Klaas and Beszteri, Bank and Gruber, Ansgar and Heijde, Marc and Katinka, Michael and Mock, Thomas and Valentin, Klaus and Verret, Fréderic and Berges, John A and Brownlee, Colin and Cadoret, Jean-Paul and Chiovitti, Anthony and Choi, Chang Jae and Coesel, Sacha and De Martino, Alessandra and Detter, J Chris and Durkin, Colleen and Falciatore, Angela and Fournet, Jérome and Haruta, Miyoshi and Huysman, Marie and Jenkins, Bethany D and Jiroutova, Katerina and Jorgensen, Richard E and Joubert, Yolaine and Kaplan, Aaron and Kröger, Nils and Kroth, Peter G and La Roche, Julie and Lindquist, Erica and Lommer, Markus and Martin-Jézéquel, Véronique and Lopez, Pascal J and Lucas, Susan and Mangogna, Manuela and McGinnis, Karen and Medlin, Linda K and Montsant, Anton and Oudot-Le Secq, Marie-Pierre and Napoli, Carolyn and Obornik, Miroslav and Parker, Micaela Schnitzler and Petit, Jean-Louis and Porcel, Betina M and Poulsen, Nicole and Robison, Matthew and Rychlewski, Leszek and Rynearson, Tatiana A and Schmutz, Jeremy and Shapiro, Harris and Siaut, Magali and Stanley, Michele and Sussman, Michael R and Taylor, Alison R and Vardi, Assaf and von Dassow, Peter and Vyverman, Wim and Willis, Anusuya and Wyrwicz, Lucjan S and Rokhsar, Daniel S and Weissenbach, Jean and Armbrust, E Virginia and Green, Beverley R and Van de Peer, Yves and Grigoriev, Igor V},
  issn         = {0028-0836},
  journal      = {NATURE},
  keywords     = {THALASSIOSIRA-PSEUDONANA,RECIPROCAL GENE LOSS,BACILLARIOPHYCEAE,METABOLISM,MECHANISMS,COMPONENTS,BACTERIA,YEASTS},
  language     = {eng},
  number       = {7219},
  pages        = {239--244},
  title        = {The Phaeodactylum genome reveals the evolutionary history of diatom genomes},
  url          = {http://dx.doi.org/10.1038/nature07410},
  volume       = {456},
  year         = {2008},
}

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